From: Berk Hess Date: Thu, 26 Apr 2012 15:40:34 +0000 (+0200) Subject: Merge release-4-5-patches into release-4-6 X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=6b2e8ac3396fc39c263ec922688ff1068f9cbf22;p=alexxy%2Fgromacs.git Merge release-4-5-patches into release-4-6 Change-Id: Id1c62a482c6c3467704cc9b657b53f7df493b7ba --- 6b2e8ac3396fc39c263ec922688ff1068f9cbf22 diff --cc CMakeLists.txt index 0218f6d73b,8fd987745f..b4af587c31 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@@ -305,7 -347,7 +305,8 @@@ check_function_exists(fsyn check_function_exists(_fileno HAVE__FILENO) check_function_exists(fileno HAVE_FILENO) check_function_exists(_commit HAVE__COMMIT) + check_function_exists(lstat HAVE_LSTAT) +check_function_exists(sigaction HAVE_SIGACTION) include(CheckLibraryExists) check_library_exists(m sqrt "" HAVE_LIBM) diff --cc share/html/online/mdp_opt.html index 3dcad45bd4,170cf9478d..bf9057abd7 --- a/share/html/online/mdp_opt.html +++ b/share/html/online/mdp_opt.html @@@ -503,17 -504,22 +504,17 @@@ might try 0.15 nm. When running in para parallelizes better than the FFT, so try decreasing grid dimensions while increasing interpolation. -

PPPM

Particle-Particle Particle-Mesh algorithm for long range -electrostatic interactions. -Use for example rlist=0.9, rcoulomb=0.9. -The grid dimensions are controlled by fourierspacing. -Reasonable grid spacing for PPPM is 0.05-0.1 nm. -See Shift for the details of the particle-particle potential. -
-NOTE: PPPM is not functional in the current version, but we plan to implement -PPPM through a small modification of the PME code.

P3M-AD

Particle-Particle Particle-Mesh algorithm with analytical derivative +for for long range electrostatic interactions. The method and code +is identical to SPME, except that the influence function is optimized +for the grid. This gives a slight increase in accuracy.

Reaction-Field

Reaction-Field electrostaticsreaction-field electrostatics

Reaction field with Coulomb cut-off rcoulomb, where rcoulomb ≥ rlist. -The dielectric constant beyond the cut-off is epsilon_rf. -The dielectric constant can be set to infinity by setting epsilon_rf=0.

+The dielectric constant beyond the cut-off is epsilon-rf. +The dielectric constant can be set to infinity by setting epsilon-rf=0.

Generalized-Reaction-Field

Generalized reaction field with Coulomb cut-off rcoulomb, @@@ -721,13 -727,14 +722,14 @@@ energy group pairs

Ewald

fourierspacing: (0.12) [nm]

The maximum grid spacing for the FFT grid when using PME or P3M. - For ordinary Ewald the spacing times the box dimensions determines the - highest magnitude to use in each direction. In all cases - each direction can be overridden by entering a non-zero value for - fourier-n[xyz]. +

For ordinary Ewald, the ratio of the box dimensions and the spacing + determines a lower bound for the number of wave vectors to use in each -(signed) direction. For PME and PPPM, that ratio determines a lower bound ++(signed) direction. For PME and P3M, that ratio determines a lower bound + for the number of Fourier-space grid points that will be used along that + axis. In all cases, the number for each direction can be overridden by + entering a non-zero value for fourier_n[xyz]. For optimizing the relative load of the particle-particle interactions - and the mesh part of PME it is useful to know that + and the mesh part of PME, it is useful to know that the accuracy of the electrostatics remains nearly constant when the Coulomb cut-off and the PME grid spacing are scaled by the same factor.

disre:

no: no distance restraints (ignore distance - restraint information in topology file); ignore distance restraint information in topology file
simple: simple (per-molecule) distance restraints, - ensemble averaging can be performed with mdrun -multi - where the environment variable GMX_DISRE_ENSEMBLE_SIZE sets the number - of systems within each ensemble (usually equal to the mdrun -multi value); simple (per-molecule) distance restraints.
ensemble: distance restraints over an ensemble of molecules in one simulation box, - should only be used for special cases, such as dimers - (this option is not fuctional in the current version of GROMACS); distance restraints over an ensemble of molecules in one + simulation box. Normally, one would perform ensemble averaging over + multiple subsystems, each in a separate box, using mdrun -multi;s + upply topol0.tpr, topol1.tpr, ... with different + coordinates and/or velocities. + The environment variable GMX_DISRE_ENSEMBLE_SIZE sets the number + of systems within each ensemble (usually equal to the mdrun -multi value).

disre_weighting:

disre-weighting:

equal (default): divide the restraint force equally over all atom pairs in the restraint
conservative: the forces are the derivative of the restraint potential, - this results in an r^-7 weighting of the atom pairs
equal: divide the restraint force equally over all atom pairs in the restraint

++The forces are conservative when disre-tau is zero. -

disre_mixed:

disre-mixed:

no: the violation used in the calculation of the restraint force is the - time averaged violation

yes

the violation used in the calculation of the restraint force is the - square root of the time averaged violation times the instantaneous violation

+ square root of the product of the time-averaged violation and the instantaneous violation -

disre_fc: (1000) [kJ mol^-1 nm^-2]

disre-fc: (1000) [kJ mol^-1 nm^-2]

force constant for distance restraints, which is multiplied by a - (possibly) different factor for each restraint

+ (possibly) different factor for each restraint given in the fac + column of the interaction in the topology file. -

disre_tau: (0) [ps]

disre-tau: (0) [ps]

time constant for distance restraints running average

time constant for distance restraints running average. A value of zero turns off time averaging.

nstdisreout: (100) [steps]

frequency to write the running time averaged and instantaneous distances - of all atom pairs involved in restraints to the energy file +

period between steps when the running time-averaged and instantaneous distances + of all atom pairs involved in restraints are written to the energy file (can make the energy file very large)

@@@ -1339,27 -1348,30 +1343,30 @@@

use orientation restraints, ensemble averaging can be performed with mdrun -multi

orire_fc: (0) [kJ mol]

orire-fc: (0) [kJ mol]

force constant for orientation restraints, which is multiplied by a - (possibly) different factor for each restraint, can be set to zero to + (possibly) different weight factor for each restraint, can be set to zero to obtain the orientations from a free simulation

orire_tau: (0) [ps]

orire-tau: (0) [ps]

time constant for orientation restraints running average

time constant for orientation restraints running average. A value of zero turns off time averaging.

orire_fitgrp:

orire-fitgrp:

fit group for orientation restraining, for a protein backbone is a good +