snew(md->tmp_r, md->mde_n);
snew(md->tmp_v, md->mde_n);
+ // TODO redo the group name memory management to make it more clear
char **grpnms;
- snew(grpnms, md->mde_n);
+ snew(grpnms, std::max(md->mde_n, md->mdeb_n)); // Just in case md->mdeb_n > md->mde_n
for (i = 0; (i < md->nTC); i++)
{
}
md->itemp = get_ebin_space(md->ebin, md->nTC, grpnms,
unit_temp_K);
+ for (i = 0; i < md->nTC; i++)
+ {
+ sfree(grpnms[i]);
+ }
+ int allocated = 0;
if (md->etc == etcNOSEHOOVER)
{
if (md->bPrintNHChains)
}
md->itc = get_ebin_space(md->ebin, md->mde_n,
grpnms, unit_invtime);
+ allocated = md->mde_n;
if (md->bMTTK)
{
for (i = 0; (i < md->nTCP); i++)
}
md->itcb = get_ebin_space(md->ebin, md->mdeb_n,
grpnms, unit_invtime);
+ allocated = md->mdeb_n;
}
}
else
}
md->itc = get_ebin_space(md->ebin, md->mde_n,
grpnms, unit_invtime);
+ allocated = md->mde_n;
}
}
}
sprintf(buf, "Lamb-%s", *(groups->groupNames[ni]));
grpnms[i] = gmx_strdup(buf);
}
- md->itc = get_ebin_space(md->ebin, md->mde_n, grpnms, "");
+ md->itc = get_ebin_space(md->ebin, md->mde_n, grpnms, "");
+ allocated = md->mde_n;
}
- for (i = 0; i < md->mde_n; i++)
+ for (i = 0; i < allocated; i++)
{
sfree(grpnms[i]);
}
grpnms[3*i+ZZ] = gmx_strdup(buf);
}
md->iu = get_ebin_space(md->ebin, 3*md->nU, grpnms, unit_vel);
+ for (i = 0; i < 3*md->nU; i++)
+ {
+ sfree(grpnms[i]);
+ }
sfree(grpnms);
}
done_mde_delta_h_coll(mdebin->dhc);
sfree(mdebin->dE);
sfree(mdebin->temperatures);
+ if (mdebin->nE > 1 && mdebin->print_grpnms != nullptr)
+ {
+ for (int n = 0; n < mdebin->nE; n++)
+ {
+ sfree(mdebin->print_grpnms[n]);
+ }
+ sfree(mdebin->print_grpnms);
+ }
sfree(mdebin);
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+/*! \internal \file
+ * \brief
+ * Tests for energy output to log and .edr files.
+ *
+ * \todo Annealing tests.
+ * \todo Position and orientation restraints tests.
+ * \todo Average and sum in edr file test.
+ * \todo AWH output tests.
+ * \todo The log and edr outputs are currently saved to the file on the disk and then read
+ * to compare with the reference data. This will be more elegant (and run faster) when we
+ * refactor the output routines to write to a stream interface, which can already be handled
+ * in-memory when running tests.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \author Artem Zhmurov <zhmurov@gmail.com>
+ *
+ * \ingroup module_mdlib
+ */
#include "gmxpre.h"
#include "gromacs/mdlib/energyoutput.h"
+#include "config.h"
+
#include <cstdio>
+#include <cstdlib>
#include <gtest/gtest.h>
#include "gromacs/mdlib/ebin.h"
#include "gromacs/mdlib/makeconstraints.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/fcdata.h"
+#include "gromacs/mdtypes/group.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/mdatom.h"
+#include "gromacs/mdtypes/state.h"
#include "gromacs/topology/topology.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/stringutil.h"
#include "gromacs/utility/textreader.h"
#include "gromacs/utility/unique_cptr.h"
class EnergyOutputTest : public ::testing::Test
{
public:
- TestFileManager fileManager_;
-
- // Objects needed to make EnergyOutput
- t_inputrec inputrec_;
- gmx_mtop_t mtop_;
- EnergyOutput energyOutput_;
-
- // Objects needed for default energy output behavior.
- t_mdatoms mdatoms_;
- std::unique_ptr<Constraints> constraints_;
- matrix box_ = {{10, 0, 0}, {0, 10, 0}, {0, 0, 10}};
- gmx_enerdata_t enerdata_;
- tensor totalVirial_, pressure_;
-
- // TODO This will be more elegant (and run faster) when we
- // refactor the output routines to write to a stream
- // interface, which can already be handled in-memory when
- // running tests.
- std::string logFilename_;
- FILE *log_;
- unique_cptr<FILE, fcloseWrapper> logFileGuard_;
-
- TestReferenceData refData_;
- TestReferenceChecker checker_;
+ //! File manager
+ TestFileManager fileManager_;
+ //! Energy (.edr) file
+ ener_file_t energyFile_;
+ //! Input data
+ t_inputrec inputrec_;
+ //! Topology
+ gmx_mtop_t mtop_;
+ //! Energy output object
+ EnergyOutput energyOutput_;
+ //! MD atoms
+ t_mdatoms mdatoms_;
+ //! Simulation time
+ double time_;
+ //! Total mass
+ real tmass_;
+ // Potential energy data
+ gmx_enerdata_t enerdata_;
+ // Kinetic energy data (for temperatures output)
+ gmx_ekindata_t ekindata_;
+ // System state
+ t_state state_;
+ // PBC box
+ matrix box_;
+ // Virial from constraints
+ tensor constraintsVirial_;
+ // Virial from force computation
+ tensor forceVirial_;
+ // Total virial
+ tensor totalVirial_;
+ // Pressure
+ tensor pressure_;
+ //! Names for the groups.
+ std::vector<std::string> groupNameStrings_ = { "Protein", "Water", "Lipid" };
+ //! Names for the groups as C strings.
+ std::vector < std::vector < char>> groupNameCStrings_;
+ //! Handles to the names as C strings in the way needed for SimulationGroups.
+ std::vector<char *> groupNameHandles_;
+ //! Total dipole momentum
+ rvec muTotal_;
+ //! Distance and orientation restraints data
+ t_fcdata fcd_;
+ //! Communication record
+ t_commrec cr_;
+ //! Constraints object (for constraints RMSD output in case of LINCS)
+ std::unique_ptr<Constraints> constraints_;
+ //! \brief Temporary output filename
+ std::string logFilename_;
+ //! Temporary energy output filename
+ std::string edrFilename_;
+ //! Pointer to a temporary output file
+ FILE *log_;
+ //! Log file wrapper
+ unique_cptr<FILE, fcloseWrapper> logFileGuard_;
+ //! Reference data
+ TestReferenceData refData_;
+ //! Checker for reference data
+ TestReferenceChecker checker_;
EnergyOutputTest() :
logFilename_(fileManager_.getTemporaryFilePath(".log")),
- log_(std::fopen(logFilename_.c_str(), "w")), logFileGuard_(log_),
+ edrFilename_(fileManager_.getTemporaryFilePath(".edr")),
+ log_(std::fopen(logFilename_.c_str(), "w")),
+ logFileGuard_(log_),
checker_(refData_.rootChecker())
{
- energyOutput_.prepare(nullptr, &mtop_, &inputrec_, nullptr, nullptr, false);
- constraints_ = makeConstraints(mtop_, inputrec_, nullptr, false, log_, mdatoms_, nullptr,
+ // Input record
+ inputrec_.delta_t = 0.001;
+
+ // Should not be a rerun
+ inputrec_.eI = eiMD;
+ // F_EQM
+ inputrec_.bQMMM = true;
+ // F_RF_EXCL will not be tested - group scheme is not supported any more
+ inputrec_.cutoff_scheme = ecutsVERLET;
+ // F_COUL_RECIP
+ inputrec_.coulombtype = eelPME;
+ // F_LJ_RECIP
+ inputrec_.vdwtype = evdwPME;
+
+ // F_DVDL_COUL, F_DVDL_VDW, F_DVDL_BONDED, F_DVDL_RESTRAINT, F_DKDL and F_DVDL
+ inputrec_.efep = efepYES;
+ inputrec_.fepvals->separate_dvdl[efptCOUL] = true;
+ inputrec_.fepvals->separate_dvdl[efptVDW] = true;
+ inputrec_.fepvals->separate_dvdl[efptBONDED] = true;
+ inputrec_.fepvals->separate_dvdl[efptRESTRAINT] = true;
+ inputrec_.fepvals->separate_dvdl[efptMASS] = true;
+ inputrec_.fepvals->separate_dvdl[efptCOUL] = true;
+ inputrec_.fepvals->separate_dvdl[efptFEP] = true;
+
+ // F_DISPCORR and F_PDISPCORR
+ inputrec_.eDispCorr = edispcEner;
+ inputrec_.bRot = true;
+
+ // F_ECONSERVED
+ inputrec_.epc = epcBERENDSEN;
+ inputrec_.ref_p[YY][XX] = 0.0;
+ inputrec_.ref_p[ZZ][XX] = 0.0;
+ inputrec_.ref_p[ZZ][YY] = 0.0;
+ inputrec_.etc = etcNOSEHOOVER;
+
+ // Dipole (mu)
+ inputrec_.ewald_geometry = eewg3DC;
+
+ // GMX_CONSTRAINTVIR environment variable should also be
+ // set to print constraints and force virials separately.
+ //
+ // TODO extract a helper function if we ever need to do
+ // this kind of thing again.
+#if GMX_NATIVE_WINDOWS
+ _putenv_s("GMX_CONSTRAINTVIR", "true");
+#else
+ setenv("GMX_CONSTRAINTVIR", "true", 1);
+#endif
+ // To print constrain RMSD, constraints algorithm should be set to LINCS.
+ inputrec_.eConstrAlg = econtLINCS;
+
+ mtop_.bIntermolecularInteractions = false;
+
+ // Constructing molecular topology
+ gmx_moltype_t molType;
+
+ molType.atoms.nr = 2;
+
+ // F_CONSTR
+ // This must be initialized so that Constraints object can be created below.
+ InteractionList interactionListConstr;
+ interactionListConstr.iatoms.resize(NRAL(F_CONSTR) + 1);
+ interactionListConstr.iatoms[0] = 0;
+ interactionListConstr.iatoms[1] = 0;
+ interactionListConstr.iatoms[2] = 1;
+ molType.ilist.at(F_CONSTR) = interactionListConstr;
+
+ InteractionList interactionListEmpty;
+ interactionListEmpty.iatoms.resize(0);
+ molType.ilist.at(F_CONSTRNC) = interactionListEmpty;
+ molType.ilist.at(F_SETTLE) = interactionListEmpty;
+
+ // F_LJ14 and F_COUL14
+ InteractionList interactionListLJ14;
+ interactionListLJ14.iatoms.resize(NRAL(F_LJ14) + 1);
+ molType.ilist.at(F_LJ14) = interactionListLJ14;
+
+ // F_LJC14_Q
+ InteractionList interactionListLJC14Q;
+ interactionListLJC14Q.iatoms.resize(NRAL(F_LJC14_Q) + 1);
+ molType.ilist.at(F_LJC14_Q) = interactionListLJC14Q;
+
+ // TODO Do proper initialization for distance and orientation
+ // restraints and remove comments to enable their output
+ // F_DISRES
+ //InteractionList interactionListDISRES;
+ //interactionListDISRES.iatoms.resize(NRAL(F_DISRES) + 1);
+ //molType.ilist.at(F_DISRES) = interactionListDISRES;
+ //
+ // F_ORIRES
+ //InteractionList interactionListORIRES;
+ //interactionListORIRES.iatoms.resize(NRAL(F_ORIRES) + 1);
+ //molType.ilist.at(F_ORIRES) = interactionListORIRES;
+
+ mtop_.moltype.push_back(molType);
+
+ gmx_molblock_t molBlock;
+ molBlock.type = 0;
+ molBlock.nmol = 1;
+ mtop_.molblock.push_back(molBlock);
+
+ // This is to keep constraints initialization happy
+ mtop_.natoms = 2;
+ mtop_.ffparams.iparams.resize(F_NRE);
+ mtop_.ffparams.functype.resize(F_NRE);
+ mtop_.ffparams.iparams.at(F_CONSTR).constr.dA = 1.0;
+ mtop_.ffparams.iparams.at(F_CONSTR).constr.dB = 1.0;
+ mtop_.ffparams.iparams.at(F_CONSTRNC).constr.dA = 1.0;
+ mtop_.ffparams.iparams.at(F_CONSTRNC).constr.dB = 1.0;
+
+ // Groups for energy output, temperature coupling and acceleration
+ for (const auto &string : groupNameStrings_)
+ {
+ std::vector<char> cString(string.begin(), string.end());
+ // Need to add null termination
+ cString.push_back('\0');
+ groupNameCStrings_.emplace_back(cString);
+ groupNameHandles_.emplace_back(groupNameCStrings_.back().data());
+ }
+ for (auto &handle : groupNameHandles_)
+ {
+ mtop_.groups.groupNames.emplace_back(&handle);
+ }
+
+ mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput].nr = 3;
+ snew(mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput].nm_ind,
+ mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput].nr);
+ mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput].nm_ind[0] = 0;
+ mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput].nm_ind[1] = 1;
+ mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput].nm_ind[2] = 2;
+
+ mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].nr = 3;
+ snew(mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].nm_ind,
+ mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].nr);
+ mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].nm_ind[0] = 0;
+ mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].nm_ind[1] = 1;
+ mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].nm_ind[2] = 2;
+
+ mtop_.groups.groups[SimulationAtomGroupType::Acceleration].nr = 2;
+ snew(mtop_.groups.groups[SimulationAtomGroupType::Acceleration].nm_ind,
+ mtop_.groups.groups[SimulationAtomGroupType::Acceleration].nr);
+ mtop_.groups.groups[SimulationAtomGroupType::Acceleration].nm_ind[0] = 0;
+ mtop_.groups.groups[SimulationAtomGroupType::Acceleration].nm_ind[1] = 2;
+
+ // Nose-Hoover chains
+ inputrec_.bPrintNHChains = true;
+ inputrec_.opts.nhchainlength = 2;
+ state_.nosehoover_xi.resize(mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].nr*inputrec_.opts.nhchainlength);
+ state_.nosehoover_vxi.resize(mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].nr*inputrec_.opts.nhchainlength);
+
+ // This will be needed only with MTTK barostat
+ state_.nhpres_xi.resize(1*inputrec_.opts.nhchainlength);
+ state_.nhpres_vxi.resize(1*inputrec_.opts.nhchainlength);
+
+ // Group pairs
+ enerdata_.grpp.nener = mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput].nr*
+ mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput].nr;
+ for (int k = 0; k < egNR; k++)
+ {
+ snew(enerdata_.grpp.ener[k], enerdata_.grpp.nener);
+ }
+
+ // Kinetic energy and related data
+ ekindata_.tcstat.resize(mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].nr);
+ ekindata_.grpstat.resize(mtop_.groups.groups[SimulationAtomGroupType::Acceleration].nr);
+
+ // This is needed so that the ebin space will be allocated
+ inputrec_.cos_accel = 1.0;
+ // This is to keep the destructor happy (otherwise sfree() segfaults)
+ ekindata_.nthreads = 0;
+ snew(ekindata_.ekin_work_alloc, 1);
+ snew(ekindata_.ekin_work, 1);
+ snew(ekindata_.dekindl_work, 1);
+
+ // Group options for annealing output
+ inputrec_.opts.ngtc = 3;
+ snew(inputrec_.opts.ref_t, inputrec_.opts.ngtc);
+ snew(inputrec_.opts.annealing, inputrec_.opts.ngtc);
+ inputrec_.opts.annealing[0] = eannNO;
+ inputrec_.opts.annealing[1] = eannSINGLE;
+ inputrec_.opts.annealing[2] = eannPERIODIC;
+
+ // This is to keep done_inputrec happy (otherwise sfree() segfaults)
+ snew(inputrec_.opts.anneal_time, inputrec_.opts.ngtc);
+ snew(inputrec_.opts.anneal_temp, inputrec_.opts.ngtc);
+
+ // Communication record (for Constraints constructor)
+ cr_.nnodes = 1;
+ cr_.dd = nullptr;
+
+ // Constraints object (to get constraints RMSD from)
+ // TODO EnergyOutput should not take Constraints object
+ // TODO This object will always return zero as RMSD value.
+ // It is more relevant to have non-zero value for testing.
+ constraints_ = makeConstraints(mtop_, inputrec_, nullptr, false, nullptr, mdatoms_, &cr_,
nullptr, nullptr, nullptr, false);
+
+ // No position/orientation restraints
+ fcd_.disres.npair = 0;
+ fcd_.orires.nr = 0;
+
+ }
+
+ void TearDown() override
+ {
+ for (int k = 0; k < egNR; k++)
+ {
+ sfree(enerdata_.grpp.ener[k]);
+ }
}
- //! Helper function to generate synthetic data to output
- void setStepData(real testValue)
+
+ /*! \brief Helper function to generate synthetic data to output
+ *
+ * \param[in,out] testValue Base value fr energy data.
+ */
+ void setStepData(double *testValue)
{
- enerdata_.term[F_LJ] = (testValue += 0.1);
- enerdata_.term[F_COUL_SR] = (testValue += 0.1);
- enerdata_.term[F_EPOT] = (testValue += 0.1);
- enerdata_.term[F_EKIN] = (testValue += 0.1);
- enerdata_.term[F_ETOT] = (testValue += 0.1);
- enerdata_.term[F_TEMP] = (testValue += 0.1);
- enerdata_.term[F_PRES] = (testValue += 0.1);
- totalVirial_[XX][XX] = (testValue += 0.1);
- totalVirial_[XX][YY] = 0.0;
- totalVirial_[XX][ZZ] = 0.0;
- totalVirial_[YY][XX] = 0.0;
- totalVirial_[YY][YY] = (testValue += 0.1);
- totalVirial_[YY][ZZ] = 0.0;
- totalVirial_[ZZ][XX] = 0.0;
- totalVirial_[ZZ][YY] = 0.0;
- totalVirial_[ZZ][ZZ] = (testValue += 0.1);
- pressure_[XX][XX] = (testValue += 0.1);
- pressure_[XX][YY] = 0.0;
- pressure_[XX][ZZ] = 0.0;
- pressure_[YY][XX] = 0.0;
- pressure_[YY][YY] = (testValue += 0.1);
- pressure_[YY][ZZ] = 0.0;
- pressure_[ZZ][XX] = 0.0;
- pressure_[ZZ][YY] = 0.0;
- pressure_[ZZ][ZZ] = (testValue += 0.1);
+
+ time_ = (*testValue += 0.1);
+ tmass_ = (*testValue += 0.1);
+
+ enerdata_.term[F_LJ] = (*testValue += 0.1);
+ enerdata_.term[F_COUL_SR] = (*testValue += 0.1);
+ enerdata_.term[F_EPOT] = (*testValue += 0.1);
+ enerdata_.term[F_EKIN] = (*testValue += 0.1);
+ enerdata_.term[F_ETOT] = (*testValue += 0.1);
+ enerdata_.term[F_TEMP] = (*testValue += 0.1);
+ enerdata_.term[F_PRES] = (*testValue += 0.1);
+
+ enerdata_.term[F_BHAM] = (*testValue += 0.1);
+ enerdata_.term[F_EQM] = (*testValue += 0.1);
+ enerdata_.term[F_RF_EXCL] = (*testValue += 0.1);
+ enerdata_.term[F_COUL_RECIP] = (*testValue += 0.1);
+ enerdata_.term[F_LJ_RECIP] = (*testValue += 0.1);
+ enerdata_.term[F_LJ14] = (*testValue += 0.1);
+ enerdata_.term[F_COUL14] = (*testValue += 0.1);
+ enerdata_.term[F_LJC14_Q] = (*testValue += 0.1);
+ enerdata_.term[F_LJC_PAIRS_NB] = (*testValue += 0.1);
+
+ enerdata_.term[F_DVDL_COUL] = (*testValue += 0.1);
+ enerdata_.term[F_DVDL_VDW] = (*testValue += 0.1);
+ enerdata_.term[F_DVDL_BONDED] = (*testValue += 0.1);
+ enerdata_.term[F_DVDL_RESTRAINT] = (*testValue += 0.1);
+ enerdata_.term[F_DKDL] = (*testValue += 0.1);
+ enerdata_.term[F_DVDL] = (*testValue += 0.1);
+
+ enerdata_.term[F_DISPCORR] = (*testValue += 0.1);
+ enerdata_.term[F_PDISPCORR] = (*testValue += 0.1);
+ enerdata_.term[F_DISRESVIOL] = (*testValue += 0.1);
+ enerdata_.term[F_ORIRESDEV] = (*testValue += 0.1);
+ enerdata_.term[F_COM_PULL] = (*testValue += 0.1);
+ enerdata_.term[F_ECONSERVED] = (*testValue += 0.1);
+
+ // Group pairs
+ for (int i = 0; i < enerdata_.grpp.nener; i++)
+ {
+ for (int k = 0; k < egNR; k++)
+ {
+ enerdata_.grpp.ener[k][i] = (*testValue += 0.1);
+ }
+ }
+
+ // Kinetic energy and related data
+ for (int i = 0; i < mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].nr; i++)
+ {
+ ekindata_.tcstat[i].T = (*testValue += 0.1);
+ ekindata_.tcstat[i].lambda = (*testValue += 0.1);
+ }
+ for (int i = 0; i < mtop_.groups.groups[SimulationAtomGroupType::Acceleration].nr; i++)
+ {
+ ekindata_.grpstat[i].u[XX] = (*testValue += 0.1);
+ ekindata_.grpstat[i].u[YY] = (*testValue += 0.1);
+ ekindata_.grpstat[i].u[ZZ] = (*testValue += 0.1);
+ }
+
+ // This conditional is to check whether the ebin was allocated.
+ // Otherwise it will print cosacc data into the first bin.
+ if (inputrec_.cos_accel != 0)
+ {
+ ekindata_.cosacc.cos_accel = (*testValue += 0.1);
+ ekindata_.cosacc.vcos = (*testValue += 0.1);
+ }
+
+ state_.box[XX][XX] = (*testValue += 0.1);
+ state_.box[XX][YY] = (*testValue += 0.1);
+ state_.box[XX][ZZ] = (*testValue += 0.1);
+ state_.box[YY][XX] = (*testValue += 0.1);
+ state_.box[YY][YY] = (*testValue += 0.1);
+ state_.box[YY][ZZ] = (*testValue += 0.1);
+ state_.box[ZZ][XX] = (*testValue += 0.1);
+ state_.box[ZZ][YY] = (*testValue += 0.1);
+ state_.box[ZZ][ZZ] = (*testValue += 0.1);
+
+ box_[XX][XX] = (*testValue += 0.1);
+ box_[XX][YY] = (*testValue += 0.1);
+ box_[XX][ZZ] = (*testValue += 0.1);
+ box_[YY][XX] = (*testValue += 0.1);
+ box_[YY][YY] = (*testValue += 0.1);
+ box_[YY][ZZ] = (*testValue += 0.1);
+ box_[ZZ][XX] = (*testValue += 0.1);
+ box_[ZZ][YY] = (*testValue += 0.1);
+ box_[ZZ][ZZ] = (*testValue += 0.1);
+
+ constraintsVirial_[XX][XX] = (*testValue += 0.1);
+ constraintsVirial_[XX][YY] = (*testValue += 0.1);
+ constraintsVirial_[XX][ZZ] = (*testValue += 0.1);
+ constraintsVirial_[YY][XX] = (*testValue += 0.1);
+ constraintsVirial_[YY][YY] = (*testValue += 0.1);
+ constraintsVirial_[YY][ZZ] = (*testValue += 0.1);
+ constraintsVirial_[ZZ][XX] = (*testValue += 0.1);
+ constraintsVirial_[ZZ][YY] = (*testValue += 0.1);
+ constraintsVirial_[ZZ][ZZ] = (*testValue += 0.1);
+
+ forceVirial_[XX][XX] = (*testValue += 0.1);
+ forceVirial_[XX][YY] = (*testValue += 0.1);
+ forceVirial_[XX][ZZ] = (*testValue += 0.1);
+ forceVirial_[YY][XX] = (*testValue += 0.1);
+ forceVirial_[YY][YY] = (*testValue += 0.1);
+ forceVirial_[YY][ZZ] = (*testValue += 0.1);
+ forceVirial_[ZZ][XX] = (*testValue += 0.1);
+ forceVirial_[ZZ][YY] = (*testValue += 0.1);
+ forceVirial_[ZZ][ZZ] = (*testValue += 0.1);
+
+ totalVirial_[XX][XX] = (*testValue += 0.1);
+ totalVirial_[XX][YY] = (*testValue += 0.1);
+ totalVirial_[XX][ZZ] = (*testValue += 0.1);
+ totalVirial_[YY][XX] = (*testValue += 0.1);
+ totalVirial_[YY][YY] = (*testValue += 0.1);
+ totalVirial_[YY][ZZ] = (*testValue += 0.1);
+ totalVirial_[ZZ][XX] = (*testValue += 0.1);
+ totalVirial_[ZZ][YY] = (*testValue += 0.1);
+ totalVirial_[ZZ][ZZ] = (*testValue += 0.1);
+
+ pressure_[XX][XX] = (*testValue += 0.1);
+ pressure_[XX][YY] = (*testValue += 0.1);
+ pressure_[XX][ZZ] = (*testValue += 0.1);
+ pressure_[YY][XX] = (*testValue += 0.1);
+ pressure_[YY][YY] = (*testValue += 0.1);
+ pressure_[YY][ZZ] = (*testValue += 0.1);
+ pressure_[ZZ][XX] = (*testValue += 0.1);
+ pressure_[ZZ][YY] = (*testValue += 0.1);
+ pressure_[ZZ][ZZ] = (*testValue += 0.1);
+
+ muTotal_[XX] = (*testValue += 0.1);
+ muTotal_[YY] = (*testValue += 0.1);
+ muTotal_[ZZ] = (*testValue += 0.1);
+
+ state_.boxv[XX][XX] = (*testValue += 0.1);
+ state_.boxv[XX][YY] = (*testValue += 0.1);
+ state_.boxv[XX][ZZ] = (*testValue += 0.1);
+ state_.boxv[YY][XX] = (*testValue += 0.1);
+ state_.boxv[YY][YY] = (*testValue += 0.1);
+ state_.boxv[YY][ZZ] = (*testValue += 0.1);
+ state_.boxv[ZZ][XX] = (*testValue += 0.1);
+ state_.boxv[ZZ][YY] = (*testValue += 0.1);
+ state_.boxv[ZZ][ZZ] = (*testValue += 0.1);
+
+ for (int i = 0; i < inputrec_.opts.ngtc; i++)
+ {
+ inputrec_.opts.ref_t[i] = (*testValue += 0.1);
+ }
+
+ for (int k = 0; k < mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].nr*inputrec_.opts.nhchainlength; k++)
+ {
+ state_.nosehoover_xi[k] = (*testValue += 0.1);
+ state_.nosehoover_vxi[k] = (*testValue += 0.1);
+ }
+ for (int k = 0; k < inputrec_.opts.nhchainlength; k++)
+ {
+ state_.nhpres_xi[k] = (*testValue += 0.1);
+ state_.nhpres_vxi[k] = (*testValue += 0.1);
+ }
+ }
+
+ /*! \brief Check if the contents of the .edr file correspond to the reference data.
+ *
+ * The code below is based on the 'gmx dump' tool.
+ *
+ * \param[in] fileName Name of the file to check.
+ * \param[in] frameCount Number of frames to check.
+ */
+ void checkEdrFile(const char *fileName, int frameCount)
+ {
+ ener_file_t edrFile;
+ gmx_enxnm_t *energyTermsEdr = nullptr;
+ int numEnergyTermsEdr;
+
+ edrFile = open_enx(fileName, "r");
+ do_enxnms(edrFile, &numEnergyTermsEdr, &energyTermsEdr);
+ assert(energyTermsEdr);
+
+ // Check header
+ TestReferenceChecker edrFileRef(checker_.checkCompound("File", "EnergyFile"));
+ TestReferenceChecker energyTermsRef(edrFileRef.checkSequenceCompound("EnergyTerms", numEnergyTermsEdr));
+ for (int i = 0; i < numEnergyTermsEdr; i++)
+ {
+ TestReferenceChecker energyTermRef(energyTermsRef.checkCompound("EnergyTerm", nullptr));
+ energyTermRef.checkString(energyTermsEdr[i].name, "Name");
+ energyTermRef.checkString(energyTermsEdr[i].unit, "Units");
+ }
+
+ // Check frames
+ TestReferenceChecker framesRef(edrFileRef.checkSequenceCompound("Frames", frameCount));
+ t_enxframe *frameEdr;
+ snew(frameEdr, 1);
+ char buffer[22];
+ for (int frameId = 0; frameId < frameCount; frameId++)
+ {
+ bool bCont = do_enx(edrFile, frameEdr);
+ EXPECT_TRUE(bCont) << gmx::formatString("Cant read frame %d from .edr file.", frameId);
+
+ TestReferenceChecker frameRef(framesRef.checkCompound("Frame", nullptr));
+ frameRef.checkReal(frameEdr->t, "Time");
+ frameRef.checkReal(frameEdr->dt, "Timestep");
+ frameRef.checkString(gmx_step_str(frameEdr->step, buffer), "Step");
+ frameRef.checkString(gmx_step_str(frameEdr->nsum, buffer), "NumSteps");
+
+ EXPECT_EQ(frameEdr->nre, numEnergyTermsEdr) << gmx::formatString("Wrong number of energy terms in frame %d.", frameId);
+ TestReferenceChecker energyValuesRef(frameRef.checkSequenceCompound("EnergyTerms", numEnergyTermsEdr));
+ for (int i = 0; i < numEnergyTermsEdr; i++)
+ {
+ TestReferenceChecker energyValueRef(energyValuesRef.checkCompound("EnergyTerm", nullptr));
+ energyValueRef.checkString(energyTermsEdr[i].name, "Name");
+ energyValueRef.checkReal(frameEdr->ener[i].e, "Value");
+ }
+ }
+
+ free_enxnms(numEnergyTermsEdr, energyTermsEdr);
+ done_ener_file(edrFile);
+
+ free_enxframe(frameEdr);
+ sfree(frameEdr);
}
};
{
ASSERT_NE(log_, nullptr);
- // Test printing values
- energyOutput_.printStepToEnergyFile(nullptr, false, false, false, log_,
- 0, 0, eprNORMAL,
- nullptr, nullptr, nullptr, nullptr);
- // Test printing averages
- energyOutput_.printStepToEnergyFile(nullptr, false, false, false, log_,
- 0, 0, eprAVER,
- nullptr, nullptr, nullptr, nullptr);
+ // Binary output will be written to the temporary location
+ energyFile_ = open_enx(edrFilename_.c_str(), "w");
+ ASSERT_NE(energyFile_, nullptr);
+
+ energyOutput_.prepare(energyFile_, &mtop_, &inputrec_, nullptr, nullptr, false);
+
+ // Print data to log and edr files
+ energyOutput_.printStepToEnergyFile(energyFile_, true, false, false, log_,
+ 100, 1.0, eprNORMAL,
+ nullptr, &mtop_.groups, &inputrec_.opts, nullptr);
+
+ // Print data to log and edr files
+ energyOutput_.printStepToEnergyFile(energyFile_, true, false, false, log_,
+ 100, 1.0, eprAVER,
+ nullptr, &mtop_.groups, &inputrec_.opts, nullptr);
// We need to close the file before the contents are available.
logFileGuard_.reset(nullptr);
+ done_ener_file(energyFile_);
+
+ // Set tolerance
+ checker_.setDefaultTolerance(relativeToleranceAsFloatingPoint(1.0, 1.0e-5));
+
+ // Test binary output
+ checkEdrFile(edrFilename_.c_str(), 1);
+
+ // Test printed values
checker_.checkInteger(energyOutput_.numEnergyTerms(), "Number of Energy Terms");
checker_.checkString(TextReader::readFileToString(logFilename_), "log");
+
}
+
TEST_F(EnergyOutputTest, HandlesSingleStep)
{
ASSERT_NE(log_, nullptr);
+ // Binary output will be written to the tempporary location
+ energyFile_ = open_enx(edrFilename_.c_str(), "w");
+ ASSERT_NE(energyFile_, nullptr);
+
+ energyOutput_.prepare(energyFile_, &mtop_, &inputrec_, nullptr, nullptr, false);
+
// Add synthetic data for a single step
- real time = 1.0;
- real testValue = 1.0;
- setStepData(testValue);
- energyOutput_.addDataAtEnergyStep(false, true, time, 0.0, &enerdata_,
- nullptr, nullptr, nullptr, box_,
- nullptr, nullptr, totalVirial_, pressure_,
- nullptr, nullptr, constraints_.get());
-
- // Test printing values
- energyOutput_.printStepToEnergyFile(nullptr, false, false, false, log_,
- 0, 0, eprNORMAL,
- nullptr, nullptr, nullptr, nullptr);
-
- // Test printing averages
- energyOutput_.printStepToEnergyFile(nullptr, false, false, false, log_,
- 0, 0, eprAVER,
- nullptr, nullptr, nullptr, nullptr);
+ double testValue = 10.0;
+ setStepData(&testValue);
+ energyOutput_.addDataAtEnergyStep(false, true, time_, tmass_, &enerdata_,
+ &state_, nullptr, nullptr, box_,
+ constraintsVirial_, forceVirial_, totalVirial_, pressure_,
+ &ekindata_, muTotal_, constraints_.get());
+
+ energyOutput_.printStepToEnergyFile(energyFile_, true, false, false, log_,
+ 100, time_, eprNORMAL,
+ nullptr, &mtop_.groups, &inputrec_.opts, nullptr);
+
+ energyOutput_.printStepToEnergyFile(energyFile_, true, false, false, log_,
+ 100, time_, eprAVER,
+ nullptr, &mtop_.groups, &inputrec_.opts, nullptr);
// We need to close the file before the contents are available.
logFileGuard_.reset(nullptr);
+ done_ener_file(energyFile_);
+
+ // Set tolerance
+ checker_.setDefaultTolerance(relativeToleranceAsFloatingPoint(testValue, 1.0e-5));
+
+ // Test binary output
+ checkEdrFile(edrFilename_.c_str(), 1);
+
+ // Test printed values
checker_.checkInteger(energyOutput_.numEnergyTerms(), "Number of Energy Terms");
checker_.checkString(TextReader::readFileToString(logFilename_), "log");
+
}
+
TEST_F(EnergyOutputTest, HandlesTwoSteps)
{
ASSERT_NE(log_, nullptr);
- // Add synthetic data for the first step
- real time = 1.0;
- real testValue = 1.0;
- setStepData(testValue);
- energyOutput_.addDataAtEnergyStep(false, true, time, 0.0, &enerdata_,
- nullptr, nullptr, nullptr, box_,
- nullptr, nullptr, totalVirial_, pressure_,
- nullptr, nullptr, constraints_.get());
-
- // Test printing values
- energyOutput_.printStepToEnergyFile(nullptr, false, false, false, log_,
- 0, 0, eprNORMAL,
- nullptr, nullptr, nullptr, nullptr);
-
- // Add synthetic data for the second step
- time += 0.005;
- setStepData(testValue += 1.0);
- energyOutput_.addDataAtEnergyStep(false, true, time, 0.0, &enerdata_,
- nullptr, nullptr, nullptr, box_,
- nullptr, nullptr, totalVirial_, pressure_,
- nullptr, nullptr, constraints_.get());
-
- // Test printing values
- energyOutput_.printStepToEnergyFile(nullptr, false, false, false, log_,
- 0, 0, eprNORMAL,
- nullptr, nullptr, nullptr, nullptr);
-
- // Test printing averages
- energyOutput_.printStepToEnergyFile(nullptr, false, false, false, log_,
- 0, 0, eprAVER,
- nullptr, nullptr, nullptr, nullptr);
+ // Binary output will be written to the temporary location
+ energyFile_ = open_enx(edrFilename_.c_str(), "w");
+ ASSERT_NE(energyFile_, nullptr);
+
+ energyOutput_.prepare(energyFile_, &mtop_, &inputrec_, nullptr, nullptr, false);
+
+ double testValue = 1.0;
+ // Add synthetic data for a first step
+ setStepData(&testValue);
+ energyOutput_.addDataAtEnergyStep(false, true, time_, tmass_, &enerdata_,
+ &state_, nullptr, nullptr, box_,
+ constraintsVirial_, forceVirial_, totalVirial_, pressure_,
+ &ekindata_, muTotal_, constraints_.get());
+
+ energyOutput_.printStepToEnergyFile(energyFile_, true, false, false, log_,
+ 100, time_, eprNORMAL,
+ nullptr, &mtop_.groups, &inputrec_.opts, nullptr);
+ // Add synthetic data for a second step
+ setStepData(&testValue);
+ energyOutput_.addDataAtEnergyStep(false, true, time_, tmass_, &enerdata_,
+ &state_, nullptr, nullptr, box_,
+ constraintsVirial_, forceVirial_, totalVirial_, pressure_,
+ &ekindata_, muTotal_, constraints_.get());
+
+ energyOutput_.printStepToEnergyFile(energyFile_, true, false, false, log_,
+ 100, time_, eprNORMAL,
+ nullptr, &mtop_.groups, &inputrec_.opts, nullptr);
+
+ energyOutput_.printStepToEnergyFile(energyFile_, true, false, false, log_,
+ 100, time_, eprAVER,
+ nullptr, &mtop_.groups, &inputrec_.opts, nullptr);
// We need to close the file before the contents are available.
logFileGuard_.reset(nullptr);
+ done_ener_file(energyFile_);
+
+ // Set tolerance
+ checker_.setDefaultTolerance(relativeToleranceAsFloatingPoint(testValue, 1.0e-5));
+
+ // Test binary output
+ checkEdrFile(edrFilename_.c_str(), 2);
+
+ // Test printed values
checker_.checkInteger(energyOutput_.numEnergyTerms(), "Number of Energy Terms");
checker_.checkString(TextReader::readFileToString(logFilename_), "log");
}
<?xml version="1.0"?>
<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
<ReferenceData>
- <Int Name="Number of Energy Terms">26</Int>
- <String Name="log"> Energies (kJ/mol)
- LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy
+ <File Name="EnergyFile">
+ <Sequence Name="EnergyTerms">
+ <Int Name="Length">111</Int>
+ <EnergyTerm>
+ <String Name="Name">LJ-14</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coulomb-14</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ (SR)</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Disper. corr.</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coulomb (SR)</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul. recip.</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ recip.</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">COM Pull En.</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Quantum En.</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Potential</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Kinetic En.</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Total Energy</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Conserved En.</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Temperature</String>
+ <String Name="Units">K</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres. DC</String>
+ <String Name="Units">bar</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pressure</String>
+ <String Name="Units">bar</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">dVremain/dl</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">dEkin/dl</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">dVcoul/dl</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">dVvdw/dl</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">dVbonded/dl</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">dVrestraint/dl</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Constr. rmsd</String>
+ <String Name="Units"></String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Box-X</String>
+ <String Name="Units">nm</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Box-Y</String>
+ <String Name="Units">nm</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Box-Z</String>
+ <String Name="Units">nm</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Volume</String>
+ <String Name="Units">nm^3</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Density</String>
+ <String Name="Units">kg/m^3</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">pV</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Enthalpy</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ShakeVir-XX</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ShakeVir-XY</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ShakeVir-XZ</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ShakeVir-YX</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ShakeVir-YY</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ShakeVir-YZ</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ShakeVir-ZX</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ShakeVir-ZY</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ShakeVir-ZZ</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ForceVir-XX</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ForceVir-XY</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ForceVir-XZ</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ForceVir-YX</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ForceVir-YY</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ForceVir-YZ</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ForceVir-ZX</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ForceVir-ZY</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ForceVir-ZZ</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-XX</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-XY</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-XZ</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-YX</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-YY</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-YZ</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-ZX</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-ZY</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-ZZ</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-XX</String>
+ <String Name="Units">bar</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-XY</String>
+ <String Name="Units">bar</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-XZ</String>
+ <String Name="Units">bar</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-YX</String>
+ <String Name="Units">bar</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-YY</String>
+ <String Name="Units">bar</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-YZ</String>
+ <String Name="Units">bar</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-ZX</String>
+ <String Name="Units">bar</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-ZY</String>
+ <String Name="Units">bar</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-ZZ</String>
+ <String Name="Units">bar</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">#Surf*SurfTen</String>
+ <String Name="Units">bar nm</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Mu-X</String>
+ <String Name="Units">D</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Mu-Y</String>
+ <String Name="Units">D</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Mu-Z</String>
+ <String Name="Units">D</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">2CosZ*Vel-X</String>
+ <String Name="Units">nm/ps</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">1/Viscosity</String>
+ <String Name="Units">m s/kg</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-SR:Protein-Protein</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-SR:Protein-Protein</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-14:Protein-Protein</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-14:Protein-Protein</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-SR:Protein-Water</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-SR:Protein-Water</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-14:Protein-Water</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-14:Protein-Water</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-SR:Protein-Lipid</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-SR:Protein-Lipid</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-14:Protein-Lipid</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-14:Protein-Lipid</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-SR:Water-Water</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-SR:Water-Water</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-14:Water-Water</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-14:Water-Water</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-SR:Water-Lipid</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-SR:Water-Lipid</String>
+ <String Name="Units">kJ/mol</String>
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+ <String Name="log">Current ref_t for group Water: 0.0
+Current ref_t for group Lipid: 0.0
+ Energies (kJ/mol)
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0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
- Temperature Pressure (bar)
- 0.00000e+00 0.00000e+00
+ Coul. recip. LJ recip. COM Pull En. Quantum En. Potential
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+ Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
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+ dVbonded/dl dVrestraint/dl Constr. rmsd
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Not enough data recorded to report energy averages
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- 1.10000e+00 1.20000e+00 1.30000e+00 1.40000e+00 1.50000e+00
- Temperature Pressure (bar)
- 1.60000e+00 1.70000e+00
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+ <String Name="Name">LJ-SR:Water-Lipid</String>
+ <Real Name="Value">15.69999999999998</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-14:Water-Lipid</String>
+ <Real Name="Value">15.899999999999979</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-14:Water-Lipid</String>
+ <Real Name="Value">15.999999999999979</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-SR:Lipid-Lipid</String>
+ <Real Name="Value">17.099999999999994</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-SR:Lipid-Lipid</String>
+ <Real Name="Value">17.199999999999996</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-14:Lipid-Lipid</String>
+ <Real Name="Value">17.399999999999999</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-14:Lipid-Lipid</String>
+ <Real Name="Value">17.5</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">T-Protein</String>
+ <Real Name="Value">17.600000000000001</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">T-Water</String>
+ <Real Name="Value">17.800000000000004</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">T-Lipid</String>
+ <Real Name="Value">18.000000000000007</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Xi-Protein</String>
+ <Real Name="Value">25.900000000000119</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">vXi-Protein</String>
+ <Real Name="Value">26.000000000000121</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Xi-Water</String>
+ <Real Name="Value">26.100000000000122</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">vXi-Water</String>
+ <Real Name="Value">26.200000000000124</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Xi-Lipid</String>
+ <Real Name="Value">26.300000000000125</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">vXi-Lipid</String>
+ <Real Name="Value">26.400000000000126</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Ux-Protein</String>
+ <Real Name="Value">18.20000000000001</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Uy-Protein</String>
+ <Real Name="Value">18.300000000000011</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Uz-Protein</String>
+ <Real Name="Value">18.400000000000013</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Ux-Lipid</String>
+ <Real Name="Value">18.500000000000014</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Uy-Lipid</String>
+ <Real Name="Value">18.600000000000016</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Uz-Lipid</String>
+ <Real Name="Value">18.700000000000017</Real>
+ </EnergyTerm>
+ </Sequence>
+ </Frame>
+ </Sequence>
+ </File>
+ <Int Name="Number of Energy Terms">111</Int>
+ <String Name="log">Current ref_t for group Water: 25.7
+Current ref_t for group Lipid: 25.8
+ Energies (kJ/mol)
+ LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
+ 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01
+ Coul. recip. LJ recip. COM Pull En. Quantum En. Potential
+ 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01
+ Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
+ 1.06000e+01 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01
+ Pressure (bar) dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl
+ 1.09000e+01 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01
+ dVbonded/dl dVrestraint/dl Constr. rmsd
+ 1.21000e+01 1.22000e+01 0.00000e+00
<====== ############### ==>
<==== A V E R A G E S ====>
Statistics over 1 steps using 1 frames
+Current ref_t for group Water: 25.7
+Current ref_t for group Lipid: 25.8
Energies (kJ/mol)
- LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy
- 1.10000e+00 1.20000e+00 1.30000e+00 1.40000e+00 1.50000e+00
- Temperature Pressure (bar)
- 1.60000e+00 1.70000e+00
+ LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
+ 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01
+ Coul. recip. LJ recip. COM Pull En. Quantum En. Potential
+ 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01
+ Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
+ 1.06000e+01 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01
+ Pressure (bar) dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl
+ 1.09000e+01 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01
+ dVbonded/dl dVrestraint/dl Constr. rmsd
+ 1.21000e+01 1.22000e+01 0.00000e+00
+
+ Box-X Box-Y Box-Z
+ 1.99000e+01 2.03000e+01 2.07000e+01
+
+ Constraint Virial (kJ/mol)
+ 2.08000e+01 2.09000e+01 2.10000e+01
+ 2.11000e+01 2.12000e+01 2.13000e+01
+ 2.14000e+01 2.15000e+01 2.16000e+01
+
+ Force Virial (kJ/mol)
+ 2.17000e+01 2.18000e+01 2.19000e+01
+ 2.20000e+01 2.21000e+01 2.22000e+01
+ 2.23000e+01 2.24000e+01 2.25000e+01
Total Virial (kJ/mol)
- 1.80000e+00 0.00000e+00 0.00000e+00
- 0.00000e+00 1.90000e+00 0.00000e+00
- 0.00000e+00 0.00000e+00 2.00000e+00
+ 2.26000e+01 2.27000e+01 2.28000e+01
+ 2.29000e+01 2.30000e+01 2.31000e+01
+ 2.32000e+01 2.33000e+01 2.34000e+01
Pressure (bar)
- 2.10000e+00 0.00000e+00 0.00000e+00
- 0.00000e+00 2.20000e+00 0.00000e+00
- 0.00000e+00 0.00000e+00 2.30000e+00
+ 2.35000e+01 2.36000e+01 2.37000e+01
+ 2.38000e+01 2.39000e+01 2.40000e+01
+ 2.41000e+01 2.42000e+01 2.43000e+01
+
+ Total Dipole (D)
+ 2.44000e+01 2.45000e+01 2.46000e+01
+
+ Epot (kJ/mol) Coul-SR LJ-SR Coul-14 LJ-14
+Protein-Protein 1.31000e+01 1.32000e+01 1.34000e+01 1.35000e+01
+ Protein-Water 1.36000e+01 1.37000e+01 1.39000e+01 1.40000e+01
+ Protein-Lipid 1.41000e+01 1.42000e+01 1.44000e+01 1.45000e+01
+ Water-Water 1.51000e+01 1.52000e+01 1.54000e+01 1.55000e+01
+ Water-Lipid 1.56000e+01 1.57000e+01 1.59000e+01 1.60000e+01
+ Lipid-Lipid 1.71000e+01 1.72000e+01 1.74000e+01 1.75000e+01
+
+ T-Protein T-Water T-Lipid
+ 1.76000e+01 1.78000e+01 1.80000e+01
+
+ Group Ux Uy Uz
+ Protein 1.82000e+01 1.83000e+01 1.84000e+01
+ Lipid 1.85000e+01 1.86000e+01 1.87000e+01
</String>
</ReferenceData>
<?xml version="1.0"?>
<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
<ReferenceData>
- <Int Name="Number of Energy Terms">26</Int>
- <String Name="log"> Energies (kJ/mol)
- LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy
- 1.10000e+00 1.20000e+00 1.30000e+00 1.40000e+00 1.50000e+00
- Temperature Pressure (bar)
- 1.60000e+00 1.70000e+00
+ <File Name="EnergyFile">
+ <Sequence Name="EnergyTerms">
+ <Int Name="Length">111</Int>
+ <EnergyTerm>
+ <String Name="Name">LJ-14</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coulomb-14</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ (SR)</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Disper. corr.</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coulomb (SR)</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul. recip.</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ recip.</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">COM Pull En.</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Quantum En.</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Potential</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Kinetic En.</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Total Energy</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Conserved En.</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Temperature</String>
+ <String Name="Units">K</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres. DC</String>
+ <String Name="Units">bar</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pressure</String>
+ <String Name="Units">bar</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">dVremain/dl</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">dEkin/dl</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">dVcoul/dl</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">dVvdw/dl</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">dVbonded/dl</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">dVrestraint/dl</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Constr. rmsd</String>
+ <String Name="Units"></String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Box-X</String>
+ <String Name="Units">nm</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Box-Y</String>
+ <String Name="Units">nm</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Box-Z</String>
+ <String Name="Units">nm</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Volume</String>
+ <String Name="Units">nm^3</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Density</String>
+ <String Name="Units">kg/m^3</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">pV</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Enthalpy</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ShakeVir-XX</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ShakeVir-XY</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ShakeVir-XZ</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ShakeVir-YX</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ShakeVir-YY</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ShakeVir-YZ</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ShakeVir-ZX</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ShakeVir-ZY</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ShakeVir-ZZ</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ForceVir-XX</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ForceVir-XY</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ForceVir-XZ</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ForceVir-YX</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ForceVir-YY</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ForceVir-YZ</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ForceVir-ZX</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ForceVir-ZY</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">ForceVir-ZZ</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-XX</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-XY</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-XZ</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-YX</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-YY</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-YZ</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-ZX</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-ZY</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-ZZ</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-XX</String>
+ <String Name="Units">bar</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-XY</String>
+ <String Name="Units">bar</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-XZ</String>
+ <String Name="Units">bar</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-YX</String>
+ <String Name="Units">bar</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-YY</String>
+ <String Name="Units">bar</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-YZ</String>
+ <String Name="Units">bar</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-ZX</String>
+ <String Name="Units">bar</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-ZY</String>
+ <String Name="Units">bar</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-ZZ</String>
+ <String Name="Units">bar</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">#Surf*SurfTen</String>
+ <String Name="Units">bar nm</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Mu-X</String>
+ <String Name="Units">D</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Mu-Y</String>
+ <String Name="Units">D</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Mu-Z</String>
+ <String Name="Units">D</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">2CosZ*Vel-X</String>
+ <String Name="Units">nm/ps</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">1/Viscosity</String>
+ <String Name="Units">m s/kg</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-SR:Protein-Protein</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-SR:Protein-Protein</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-14:Protein-Protein</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-14:Protein-Protein</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-SR:Protein-Water</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-SR:Protein-Water</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-14:Protein-Water</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-14:Protein-Water</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-SR:Protein-Lipid</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-SR:Protein-Lipid</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-14:Protein-Lipid</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-14:Protein-Lipid</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-SR:Water-Water</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-SR:Water-Water</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-14:Water-Water</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-14:Water-Water</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-SR:Water-Lipid</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-SR:Water-Lipid</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-14:Water-Lipid</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-14:Water-Lipid</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-SR:Lipid-Lipid</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-SR:Lipid-Lipid</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-14:Lipid-Lipid</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-14:Lipid-Lipid</String>
+ <String Name="Units">kJ/mol</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">T-Protein</String>
+ <String Name="Units">K</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">T-Water</String>
+ <String Name="Units">K</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">T-Lipid</String>
+ <String Name="Units">K</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Xi-Protein</String>
+ <String Name="Units">1/ps</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">vXi-Protein</String>
+ <String Name="Units">1/ps</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Xi-Water</String>
+ <String Name="Units">1/ps</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">vXi-Water</String>
+ <String Name="Units">1/ps</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Xi-Lipid</String>
+ <String Name="Units">1/ps</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">vXi-Lipid</String>
+ <String Name="Units">1/ps</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Ux-Protein</String>
+ <String Name="Units">nm/ps</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Uy-Protein</String>
+ <String Name="Units">nm/ps</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Uz-Protein</String>
+ <String Name="Units">nm/ps</String>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Ux-Lipid</String>
+ <String Name="Units">nm/ps</String>
+ </EnergyTerm>
+ <EnergyTerm>
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+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-YX</String>
+ <Real Name="Value">31.300000000000178</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-YY</String>
+ <Real Name="Value">31.40000000000018</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-YZ</String>
+ <Real Name="Value">31.500000000000181</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-ZX</String>
+ <Real Name="Value">31.600000000000183</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-ZY</String>
+ <Real Name="Value">31.700000000000184</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Vir-ZZ</String>
+ <Real Name="Value">31.800000000000185</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-XX</String>
+ <Real Name="Value">31.900000000000187</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-XY</String>
+ <Real Name="Value">32.000000000000185</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-XZ</String>
+ <Real Name="Value">32.100000000000186</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-YX</String>
+ <Real Name="Value">32.200000000000188</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-YY</String>
+ <Real Name="Value">32.300000000000189</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-YZ</String>
+ <Real Name="Value">32.40000000000019</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-ZX</String>
+ <Real Name="Value">32.500000000000192</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-ZY</String>
+ <Real Name="Value">32.600000000000193</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Pres-ZZ</String>
+ <Real Name="Value">32.700000000000195</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">#Surf*SurfTen</String>
+ <Real Name="Value">17.460000000000335</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Mu-X</String>
+ <Real Name="Value">32.800000000000196</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Mu-Y</String>
+ <Real Name="Value">32.900000000000198</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Mu-Z</String>
+ <Real Name="Value">33.000000000000199</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">2CosZ*Vel-X</String>
+ <Real Name="Value">27.300000000000122</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">1/Viscosity</String>
+ <Real Name="Value">35806907.916011348</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-SR:Protein-Protein</String>
+ <Real Name="Value">21.500000000000039</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-SR:Protein-Protein</String>
+ <Real Name="Value">21.600000000000041</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-14:Protein-Protein</String>
+ <Real Name="Value">21.800000000000043</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-14:Protein-Protein</String>
+ <Real Name="Value">21.900000000000045</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-SR:Protein-Water</String>
+ <Real Name="Value">22.000000000000046</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-SR:Protein-Water</String>
+ <Real Name="Value">22.100000000000048</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-14:Protein-Water</String>
+ <Real Name="Value">22.30000000000005</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-14:Protein-Water</String>
+ <Real Name="Value">22.400000000000052</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-SR:Protein-Lipid</String>
+ <Real Name="Value">22.500000000000053</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-SR:Protein-Lipid</String>
+ <Real Name="Value">22.600000000000055</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-14:Protein-Lipid</String>
+ <Real Name="Value">22.800000000000058</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-14:Protein-Lipid</String>
+ <Real Name="Value">22.900000000000059</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-SR:Water-Water</String>
+ <Real Name="Value">23.500000000000068</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-SR:Water-Water</String>
+ <Real Name="Value">23.600000000000069</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-14:Water-Water</String>
+ <Real Name="Value">23.800000000000072</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-14:Water-Water</String>
+ <Real Name="Value">23.900000000000073</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-SR:Water-Lipid</String>
+ <Real Name="Value">24.000000000000075</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-SR:Water-Lipid</String>
+ <Real Name="Value">24.100000000000076</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-14:Water-Lipid</String>
+ <Real Name="Value">24.300000000000079</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-14:Water-Lipid</String>
+ <Real Name="Value">24.40000000000008</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-SR:Lipid-Lipid</String>
+ <Real Name="Value">25.500000000000096</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-SR:Lipid-Lipid</String>
+ <Real Name="Value">25.600000000000097</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Coul-14:Lipid-Lipid</String>
+ <Real Name="Value">25.8000000000001</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">LJ-14:Lipid-Lipid</String>
+ <Real Name="Value">25.900000000000102</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">T-Protein</String>
+ <Real Name="Value">26.000000000000103</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">T-Water</String>
+ <Real Name="Value">26.200000000000106</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">T-Lipid</String>
+ <Real Name="Value">26.400000000000109</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Xi-Protein</String>
+ <Real Name="Value">34.300000000000217</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">vXi-Protein</String>
+ <Real Name="Value">34.400000000000219</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Xi-Water</String>
+ <Real Name="Value">34.50000000000022</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">vXi-Water</String>
+ <Real Name="Value">34.600000000000222</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Xi-Lipid</String>
+ <Real Name="Value">34.700000000000223</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">vXi-Lipid</String>
+ <Real Name="Value">34.800000000000225</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Ux-Protein</String>
+ <Real Name="Value">26.600000000000112</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Uy-Protein</String>
+ <Real Name="Value">26.700000000000113</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Uz-Protein</String>
+ <Real Name="Value">26.800000000000114</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Ux-Lipid</String>
+ <Real Name="Value">26.900000000000116</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Uy-Lipid</String>
+ <Real Name="Value">27.000000000000117</Real>
+ </EnergyTerm>
+ <EnergyTerm>
+ <String Name="Name">Uz-Lipid</String>
+ <Real Name="Value">27.100000000000119</Real>
+ </EnergyTerm>
+ </Sequence>
+ </Frame>
+ </Sequence>
+ </File>
+ <Int Name="Number of Energy Terms">111</Int>
+ <String Name="log">Current ref_t for group Water: 16.7
+Current ref_t for group Lipid: 16.8
+ Energies (kJ/mol)
+ LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
+ 2.50000e+00 2.60000e+00 1.30000e+00 3.50000e+00 1.40000e+00
+ Coul. recip. LJ recip. COM Pull En. Quantum En. Potential
+ 2.30000e+00 2.40000e+00 3.90000e+00 2.10000e+00 1.50000e+00
+ Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
+ 1.60000e+00 1.70000e+00 4.00000e+00 1.80000e+00 3.60000e+00
+ Pressure (bar) dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl
+ 1.90000e+00 3.40000e+00 3.30000e+00 2.90000e+00 3.00000e+00
+ dVbonded/dl dVrestraint/dl Constr. rmsd
+ 3.10000e+00 3.20000e+00 0.00000e+00
+Current ref_t for group Water: 34.1
+Current ref_t for group Lipid: 34.2
Energies (kJ/mol)
- LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy
- 2.10000e+00 2.20000e+00 2.30000e+00 2.40000e+00 2.50000e+00
- Temperature Pressure (bar)
- 2.60000e+00 2.70000e+00
+ LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
+ 1.99000e+01 2.00000e+01 1.87000e+01 2.09000e+01 1.88000e+01
+ Coul. recip. LJ recip. COM Pull En. Quantum En. Potential
+ 1.97000e+01 1.98000e+01 2.13000e+01 1.95000e+01 1.89000e+01
+ Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
+ 1.90000e+01 1.91000e+01 2.14000e+01 1.92000e+01 2.10000e+01
+ Pressure (bar) dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl
+ 1.93000e+01 2.08000e+01 2.07000e+01 2.03000e+01 2.04000e+01
+ dVbonded/dl dVrestraint/dl Constr. rmsd
+ 2.05000e+01 2.06000e+01 0.00000e+00
<====== ############### ==>
<==== A V E R A G E S ====>
Statistics over 2 steps using 2 frames
+Current ref_t for group Water: 34.1
+Current ref_t for group Lipid: 34.2
Energies (kJ/mol)
- LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy
- 1.60000e+00 1.70000e+00 1.80000e+00 1.90000e+00 2.00000e+00
- Temperature Pressure (bar)
- 2.10000e+00 2.20000e+00
+ LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
+ 1.12000e+01 1.13000e+01 1.00000e+01 1.22000e+01 1.01000e+01
+ Coul. recip. LJ recip. COM Pull En. Quantum En. Potential
+ 1.10000e+01 1.11000e+01 1.26000e+01 1.08000e+01 1.02000e+01
+ Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
+ 1.03000e+01 1.04000e+01 1.27000e+01 1.05000e+01 1.23000e+01
+ Pressure (bar) dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl
+ 1.06000e+01 1.21000e+01 1.20000e+01 1.16000e+01 1.17000e+01
+ dVbonded/dl dVrestraint/dl Constr. rmsd
+ 1.18000e+01 1.19000e+01 0.00000e+00
+
+ Box-X Box-Y Box-Z
+ 1.96000e+01 2.00000e+01 2.04000e+01
+
+ Constraint Virial (kJ/mol)
+ 2.05000e+01 2.06000e+01 2.07000e+01
+ 2.08000e+01 2.09000e+01 2.10000e+01
+ 2.11000e+01 2.12000e+01 2.13000e+01
+
+ Force Virial (kJ/mol)
+ 2.14000e+01 2.15000e+01 2.16000e+01
+ 2.17000e+01 2.18000e+01 2.19000e+01
+ 2.20000e+01 2.21000e+01 2.22000e+01
Total Virial (kJ/mol)
- 2.30000e+00 0.00000e+00 0.00000e+00
- 0.00000e+00 2.40000e+00 0.00000e+00
- 0.00000e+00 0.00000e+00 2.50000e+00
+ 2.23000e+01 2.24000e+01 2.25000e+01
+ 2.26000e+01 2.27000e+01 2.28000e+01
+ 2.29000e+01 2.30000e+01 2.31000e+01
Pressure (bar)
- 2.60000e+00 0.00000e+00 0.00000e+00
- 0.00000e+00 2.70000e+00 0.00000e+00
- 0.00000e+00 0.00000e+00 2.80000e+00
+ 2.32000e+01 2.33000e+01 2.34000e+01
+ 2.35000e+01 2.36000e+01 2.37000e+01
+ 2.38000e+01 2.39000e+01 2.40000e+01
+
+ Total Dipole (D)
+ 2.41000e+01 2.42000e+01 2.43000e+01
+
+ Epot (kJ/mol) Coul-SR LJ-SR Coul-14 LJ-14
+Protein-Protein 1.28000e+01 1.29000e+01 1.31000e+01 1.32000e+01
+ Protein-Water 1.33000e+01 1.34000e+01 1.36000e+01 1.37000e+01
+ Protein-Lipid 1.38000e+01 1.39000e+01 1.41000e+01 1.42000e+01
+ Water-Water 1.48000e+01 1.49000e+01 1.51000e+01 1.52000e+01
+ Water-Lipid 1.53000e+01 1.54000e+01 1.56000e+01 1.57000e+01
+ Lipid-Lipid 1.68000e+01 1.69000e+01 1.71000e+01 1.72000e+01
+
+ T-Protein T-Water T-Lipid
+ 1.73000e+01 1.75000e+01 1.77000e+01
+
+ Group Ux Uy Uz
+ Protein 1.79000e+01 1.80000e+01 1.81000e+01
+ Lipid 1.82000e+01 1.83000e+01 1.84000e+01
</String>
</ReferenceData>
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff