To avoid spurious contibrutions to the virial and pressure due to large
forces between completely frozen atoms you need to use
<A HREF="#egexcl">energy group exclusions</A>, this also saves computing time.
-Note that frozen coordinates are not subject to pressure scaling.</dd>
+Note that coordinates of frozen atoms are not scaled by pressure-coupling
+algorithms.</dd>
<dt><b>freezedim: </b></dt>
<dd>dimensions for which groups in <b>freezegrps</b> should be frozen,
specify <tt>Y</tt> or <tt>N</tt> for X, Y and Z and for each group
static void cp_error()
{
- gmx_fatal(FARGS,"Checkpoint file corrupted/truncated, or maybe you are out of quota?");
+ gmx_fatal(FARGS,"Checkpoint file corrupted/truncated, or maybe you are out of disk space?");
}
static void do_cpt_string_err(XDR *xd,gmx_bool bRead,const char *desc,char **s,FILE *list)
res = xdr_int(xd,&magic);
if (res == 0)
{
- gmx_fatal(FARGS,"The checkpoint file is empty/corrupted, or maybe you are out of quota?");
+ gmx_fatal(FARGS,"The checkpoint file is empty/corrupted, or maybe you are out of disk space?");
}
if (magic != CPT_MAGIC1)
{
(do_cpt_files(gmx_fio_getxdr(fp),FALSE,&outputfiles,&noutputfiles,NULL,
file_version) < 0))
{
- gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of quota?");
+ gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
}
do_cpt_footer(gmx_fio_getxdr(fp),FALSE,file_version);
{
char buf[STRLEN];
sprintf(buf,
- "Cannot fsync '%s'; maybe you are out of disk space or quota?",
+ "Cannot fsync '%s'; maybe you are out of disk space?",
gmx_fio_getname(ret));
if (getenv(GMX_IGNORE_FSYNC_FAILURE_ENV)==NULL)
if( gmx_fio_close(fp) != 0)
{
- gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of quota?");
+ gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
}
/* we don't move the checkpoint if the user specified they didn't want it,
}
if (gmx_file_rename(fntemp, fn) != 0)
{
- gmx_file("Cannot rename checkpoint file; maybe you are out of quota?");
+ gmx_file("Cannot rename checkpoint file; maybe you are out of disk space?");
}
}
}
if( gmx_fio_close(fp) != 0)
{
- gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of quota?");
+ gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
}
sfree(fprog);
read_checkpoint_data(fp,simulation_part,step,t,state,FALSE,NULL,NULL);
if( gmx_fio_close(fp) != 0)
{
- gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of quota?");
+ gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
}
}
}
if( gmx_fio_close(fp) != 0)
{
- gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of quota?");
+ gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
}
done_state(&state);
&nfiles,&outputfiles);
if( gmx_fio_close(fp) != 0)
{
- gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of quota?");
+ gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
}
done_state(&state);
}
if(!xdr_string(xdr,&(nm->name),STRLEN))
{
- gmx_file("Cannot write energy names to file; maybe you are out of quota?");
+ gmx_file("Cannot write energy names to file; maybe you are out of disk space?");
}
if (file_version >= 2)
{
if(!xdr_string(xdr,&(nm->unit),STRLEN))
{
- gmx_file("Cannot write energy names to file; maybe you are out of quota?");
+ gmx_file("Cannot write energy names to file; maybe you are out of disk space?");
}
}
else
{
if(!bRead)
{
- gmx_file("Cannot write energy names to file; maybe you are out of quota?");
+ gmx_file("Cannot write energy names to file; maybe you are out of disk space?");
}
*nre=0;
return;
{
if(gmx_fio_close(ef->fio) != 0)
{
- gmx_file("Cannot close energy file; it might be corrupt, or maybe you are out of quota?");
+ gmx_file("Cannot close energy file; it might be corrupt, or maybe you are out of disk space?");
}
}
do_eheader(ef,&file_version,fr,nre,&bWrongPrecision,&bOK);
if(!bOK)
{
- gmx_file("Cannot write energy file header; maybe you are out of quota?");
+ gmx_file("Cannot write energy file header; maybe you are out of disk space?");
}
if (((fr->e_size && (fr->nre == nre) &&
}
else
{
- gmx_file("Cannot write energy file header; maybe you are out of quota?");
+ gmx_file("Cannot write energy file header; maybe you are out of disk space?");
}
return FALSE;
}
{
if( gmx_fio_flush(ef->fio) != 0)
{
- gmx_file("Cannot write energy file; maybe you are out of quota?");
+ gmx_file("Cannot write energy file; maybe you are out of disk space?");
}
}
char buf[STRLEN];
sprintf(
buf,
- "Cannot write file '%s'; maybe you are out of disk space or quota?",
+ "Cannot write file '%s'; maybe you are out of disk space?",
fio->fn);
gmx_file(buf);
}
gmx_bool bSelDump = FALSE;
t_pargs sel_pa[] = {
{"-select", FALSE, etSTR, {&selection},
- "Selection string (use 'help' for help)"},
+ "Selection string (use 'help' for help). Note that the "
+ "whole selection string will need to be quoted so that "
+ "your shell will pass it in as a string. Example: "
+ "[TT]g_select -select '\"Nearby water\" resname SOL "
+ "and within 0.25 of group Protein'[tt]"},
{"-seldebug", FALSE, etBOOL, {&bSelDump},
"HIDDENPrint out the parsed and compiled selection trees"},
};
{
if( do_trn(fio,FALSE,&step,&t,&lambda,box,&natoms,x,v,f) == FALSE)
{
- gmx_file("Cannot write trajectory frame; maybe you are out of quota?");
+ gmx_file("Cannot write trajectory frame; maybe you are out of disk space?");
}
}
{ "[grk]", "}" },
{ "[MATH]","\\ensuremath{" },
{ "[math]","}" },
+ { "[CHEVRON]", "\\ensuremath{<}" },
+ { "[chevron]", "\\ensuremath{>}" },
+ { "[MAG]", "\\ensuremath{|}" },
+ { "[mag]", "\\ensuremath{|}" },
{ "[INT]","\\ensuremath{\\int" },
{ "[FROM]","_" },
{ "[from]","" },
{ "[SINH]","\\ensuremath{\\sinh{(" },
{ "[sinh]",")}}" },
{ "[TANH]","\\ensuremath{\\tanh{(" },
- { "[tanh]",")}}" },
- /* The next two lines used to substitute "|" and "||" to "or", but only
- * g_angle used that functionality, so that was changed to a textual
- * "or" there, so that other places could use those symbols to indicate
- * magnitudes. */
- { "||", "\\textbar{}\\textbar" },
- { "|", "\\textbar{}" }
+ { "[tanh]",")}}" }
};
#define NSRTEX asize(sandrTeX)
{ "[it]", "" },
{ "[MATH]","" },
{ "[math]","" },
+ { "[CHEVRON]","<" },
+ { "[chevron]",">" },
+ { "[MAG]", "|" },
+ { "[mag]", "|" },
{ "[INT]","integral" },
{ "[FROM]"," from " },
{ "[from]","" },
{ "[it]", "''" },
{ "[MATH]","" },
{ "[math]","" },
+ { "[CHEVRON]","<" },
+ { "[chevron]",">" },
+ { "[MAG]", "|" },
+ { "[mag]", "|" },
{ "[INT]","integral" },
{ "[FROM]"," from " },
{ "[from]","" },
{ "[it]", "\\fR" },
{ "[MATH]","" },
{ "[math]","" },
+ { "[CHEVRON]","<" },
+ { "[chevron]",">" },
+ { "[MAG]", "|" },
+ { "[mag]", "|" },
{ "[INT]","integral" },
{ "[FROM]"," from " },
{ "[from]","" },
{ "[it]", "</it>" },
{ "[MATH]","" },
{ "[math]","" },
+ { "[CHEVRON]","<" },
+ { "[chevron]",">" },
+ { "[MAG]", "|" },
+ { "[mag]", "|" },
{ "[INT]","integral" },
{ "[FROM]"," from " },
{ "[from]","" },
{ "[it]", "</it>" },
{ "[MATH]","" },
{ "[math]","" },
+ { "[CHEVRON]","<" },
+ { "[chevron]",">" },
+ { "[MAG]", "|" },
+ { "[mag]", "|" },
{ "[INT]","integral" },
{ "[FROM]"," from " },
{ "[from]","" },
{ "-rmsd", FALSE, etBOOL, {&bRMSD},
"Print RMSD for x, v and f" },
{ "-tol", FALSE, etREAL, {&ftol},
- "Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|)" },
+ "Relative tolerance for comparing real values defined as [MATH]2*(a-b)/([MAG]a[mag]+[MAG]b[mag])[math]" },
{ "-abstol", FALSE, etREAL, {&abstol},
"Absolute tolerance, useful when sums are close to zero." },
{ "-ab", FALSE, etBOOL, {&bCompAB},
{
if(fflush(fplog) != 0)
{
- gmx_fatal(FARGS,"Cannot flush logfile - maybe you are out of quota?");
+ gmx_fatal(FARGS,"Cannot flush logfile - maybe you are out of disk space?");
}
}
}
{
if (fflush(fplog) != 0)
{
- gmx_fatal(FARGS,"Cannot flush logfile - maybe you are out of quota?");
+ gmx_fatal(FARGS,"Cannot flush logfile - maybe you are out of disk space?");
}
}
{ "-multi", FALSE, etINT,{&nmultisim},
"Do multiple simulations in parallel" },
{ "-replex", FALSE, etINT, {&repl_ex_nst},
- "Attempt replica exchange periodically with this period" },
+ "Attempt replica exchange periodically with this period (steps)" },
{ "-reseed", FALSE, etINT, {&repl_ex_seed},
"Seed for replica exchange, -1 is generate a seed" },
{ "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
constr->lagr_nalloc = over_alloc_dd(ncons);
srenew(constr->lagr,constr->lagr_nalloc);
}
-
- constr->shaked = shake_init();
}
}
{
please_cite(fplog,"Barth95a");
}
+
+ constr->shaked = shake_init();
}
}
}
if (rc < 0)
{
- gmx_fatal(FARGS,"Cannot write to logfile; maybe you are out of quota?");
+ gmx_fatal(FARGS,"Cannot write to logfile; maybe you are out of disk space?");
}
}
(mdof_flags & MDOF_F) ? f_global : NULL);
if (gmx_fio_flush(of->fp_trn) != 0)
{
- gmx_file("Cannot write trajectory; maybe you are out of quota?");
+ gmx_file("Cannot write trajectory; maybe you are out of disk space?");
}
gmx_fio_check_file_position(of->fp_trn);
}
if (write_xtc(of->fp_xtc,*n_xtc,step,t,
state_local->box,xxtc,of->xtc_prec) == 0)
{
- gmx_fatal(FARGS,"XTC error - maybe you are out of quota?");
+ gmx_fatal(FARGS,"XTC error - maybe you are out of disk space?");
}
gmx_fio_check_file_position(of->fp_xtc);
}
"A set is divided in a number of blocks and averages are calculated for",
"each block. The error for the total average is calculated from",
"the variance between averages of the m blocks B[SUB]i[sub] as follows:",
- "error^2 = [SUM][sum] (B[SUB]i[sub] - <B>)^2 / (m*(m-1)).",
+ "error^2 = [SUM][sum] (B[SUB]i[sub] - [CHEVRON]B[chevron])^2 / (m*(m-1)).",
"These errors are plotted as a function of the block size.",
"Also an analytical block average curve is plotted, assuming",
"that the autocorrelation is a sum of two exponentials.",
"The distributions [TT](histo-(dihedral)(RESIDUE).xvg[tt]) are cumulative over all residues of each type.[PAR]",
"If option [TT]-corr[tt] is given, the program will",
"calculate dihedral autocorrelation functions. The function used",
- "is C(t) = < [COS][GRK]chi[grk]([GRK]tau[grk])[cos] [COS][GRK]chi[grk]([GRK]tau[grk]+t)[cos] >. The use of cosines",
+ "is C(t) = [CHEVRON][COS][GRK]chi[grk]([GRK]tau[grk])[cos] [COS][GRK]chi[grk]([GRK]tau[grk]+t)[cos][chevron]. The use of cosines",
"rather than angles themselves, resolves the problem of periodicity.",
"(Van der Spoel & Berendsen (1997), Biophys. J. 72, 2032-2041).",
"Separate files for each dihedral of each residue",
{ "-dista", FALSE, etBOOL, {&bRMSdist},
"Use RMSD of distances instead of RMS deviation" },
{ "-nlevels",FALSE,etINT, {&nlevels},
- "Discretize RMSD matrix in # levels" },
+ "Discretize RMSD matrix in this number of levels" },
{ "-cutoff",FALSE, etREAL, {&rmsdcut},
"RMSD cut-off (nm) for two structures to be neighbor" },
{ "-fit", FALSE, etBOOL, {&bFit},
{ "-av", FALSE, etBOOL, {&bAverage},
"Write average iso middle structure for each cluster" },
{ "-wcl", FALSE, etINT, {&write_ncl},
- "Write all structures for first # clusters to numbered files" },
+ "Write the structures for this number of clusters to numbered files" },
{ "-nst", FALSE, etINT, {&write_nst},
- "Only write all structures if more than # per cluster" },
+ "Only write all structures if more than this number of structures per cluster" },
{ "-rmsmin",FALSE, etREAL, {&rmsmin},
"minimum rms difference with rest of cluster for writing structures" },
{ "-method",FALSE, etENUM, {methodname},
{ "-d", FALSE, etSTR, {&axtitle},
"Take the normal on the membrane in direction X, Y or Z." },
{ "-sl", FALSE, etINT, {&nslices},
- "Divide the box in #nr slices." },
+ "Divide the box in this number of slices." },
{ "-dens", FALSE, etENUM, {dens_opt},
"Density"},
{ "-ng", FALSE, etINT, {&ngrps},
- "Number of groups to compute densities of" },
+ "Number of groups of which to compute densities." },
{ "-symm", FALSE, etBOOL, {&bSymmetrize},
"Symmetrize the density along the axis, with respect to the center. Useful for bilayers." },
{ "-center", FALSE, etBOOL, {&bCenter},
"center of mass of the molecule.[PAR]",
"The file [TT]Mtot.xvg[tt] contains the total dipole moment of a frame, the",
"components as well as the norm of the vector.",
- "The file [TT]aver.xvg[tt] contains < |[GRK]mu[grk]|^2 > and |< [GRK]mu[grk] >|^2 during the",
+ "The file [TT]aver.xvg[tt] contains [CHEVRON][MAG][GRK]mu[grk][mag]^2[chevron] and [MAG][CHEVRON][GRK]mu[grk][chevron][mag]^2 during the",
"simulation.",
"The file [TT]dipdist.xvg[tt] contains the distribution of dipole moments during",
"the simulation",
{ "-corr", FALSE, etENUM, {corrtype},
"Correlation function to calculate" },
{ "-pairs", FALSE, etBOOL, {&bPairs},
- "Calculate |cos [GRK]theta[grk]| between all pairs of molecules. May be slow" },
+ "Calculate [MAG][COS][GRK]theta[grk][cos][mag] between all pairs of molecules. May be slow" },
{ "-ncos", FALSE, etINT, {&ncos},
- "Must be 1 or 2. Determines whether the <cos> is computed between all molecules in one group, or between molecules in two different groups. This turns on the [TT]-gkr[tt] flag." },
+ "Must be 1 or 2. Determines whether the [CHEVRON][COS][GRK]theta[grk][cos][chevron] is computed between all molecules in one group, or between molecules in two different groups. This turns on the [TT]-g[tt] flag." },
{ "-axis", FALSE, etSTR, {&axtitle},
"Take the normal on the computational box in direction X, Y or Z." },
{ "-sl", FALSE, etINT, {&nslices},
- "Divide the box in #nr slices." },
+ "Divide the box into this number of slices." },
{ "-gkratom", FALSE, etINT, {&nFA},
"Use the n-th atom of a molecule (starting from 1) to calculate the distance between molecules rather than the center of charge (when 0) in the calculation of distance dependent Kirkwood factors" },
{ "-gkratom2", FALSE, etINT, {&nFB},
"calculated ([TT]-etot[tt]).[PAR]",
"An approximation of the free energy can be calculated using:",
- "[MATH]E[SUB]free[sub] = E[SUB]0[sub] + kT [LOG]<[EXP](E-E[SUB]0[sub])/kT[exp]>[log][math], where '<>'",
+ "[MATH]E[SUB]free[sub] = E[SUB]0[sub] + kT [LOG][CHEVRON][EXP](E-E[SUB]0[sub])/kT[exp][chevron][log][math], where '[MATH][CHEVRON][chevron][math]'",
"stands for time-average. A file with reference free energies",
"can be supplied to calculate the free energy difference",
"with some reference state. Group names (e.g. residue names)",
"With [TT]-fee[tt] an estimate is calculated for the free-energy",
"difference with an ideal gas state: [BR]",
- " [GRK]Delta[grk] A = A(N,V,T) - A[SUB]idealgas[sub](N,V,T) = kT [LN] < [EXP]U[SUB]pot[sub]/kT[exp] >[ln][BR]",
- " [GRK]Delta[grk] G = G(N,p,T) - G[SUB]idealgas[sub](N,p,T) = kT [LN] < [EXP]U[SUB]pot[sub]/kT[exp] >[ln][BR]",
+ " [GRK]Delta[grk] A = A(N,V,T) - A[SUB]idealgas[sub](N,V,T) = kT [LN][CHEVRON][EXP]U[SUB]pot[sub]/kT[exp][chevron][ln][BR]",
+ " [GRK]Delta[grk] G = G(N,p,T) - G[SUB]idealgas[sub](N,p,T) = kT [LN][CHEVRON][EXP]U[SUB]pot[sub]/kT[exp][chevron][ln][BR]",
"where k is Boltzmann's constant, T is set by [TT]-fetemp[tt] and",
"the average is over the ensemble (or time in a trajectory).",
"Note that this is in principle",
"only correct when averaging over the whole (Boltzmann) ensemble",
"and using the potential energy. This also allows for an entropy",
"estimate using:[BR]",
- " [GRK]Delta[grk] S(N,V,T) = S(N,V,T) - S[SUB]idealgas[sub](N,V,T) = (<U[SUB]pot[sub]> - [GRK]Delta[grk] A)/T[BR]",
- " [GRK]Delta[grk] S(N,p,T) = S(N,p,T) - S[SUB]idealgas[sub](N,p,T) = (<U[SUB]pot[sub]> + pV - [GRK]Delta[grk] G)/T",
+ " [GRK]Delta[grk] S(N,V,T) = S(N,V,T) - S[SUB]idealgas[sub](N,V,T) = ([CHEVRON]U[SUB]pot[sub][chevron] - [GRK]Delta[grk] A)/T[BR]",
+ " [GRK]Delta[grk] S(N,p,T) = S(N,p,T) - S[SUB]idealgas[sub](N,p,T) = ([CHEVRON]U[SUB]pot[sub][chevron] + pV - [GRK]Delta[grk] G)/T",
"[PAR]",
"When a second energy file is specified ([TT]-f2[tt]), a free energy",
- "difference is calculated [BR] dF = -kT [LN]< [EXP]-(E[SUB]B[sub]-E[SUB]A[sub])/kT[exp] >[SUB]A[sub][ln] ,",
+ "difference is calculated [BR] dF = -kT [LN][CHEVRON][EXP]-(E[SUB]B[sub]-E[SUB]A[sub])/kT[exp][chevron][SUB]A[sub][ln] ,",
"where E[SUB]A[sub] and E[SUB]B[sub] are the energies from the first and second energy",
"files, and the average is over the ensemble A. The running average",
"of the free energy difference is printed to a file specified by [TT]-ravg[tt].",
{ "-T", FALSE, etREAL, {&tref},
"Reference temperature for computing rate constants" },
{ "-n", FALSE, etINT, {&nreplica},
- "Read data for # replicas. Only necessary when files are written in xmgrace format using @type and & as delimiters." },
+ "Read data for this number of replicas. Only necessary when files are written in xmgrace format using @type and & as delimiters." },
{ "-cut", FALSE, etREAL, {&cutoff},
"Cut-off (max) value for regarding a structure as folded" },
{ "-ucut", FALSE, etREAL, {&ucut},
{ "-t", FALSE, etREAL, {&truncate},
"trunc distance" },
{ "-nlevels", FALSE, etINT, {&nlevels},
- "Discretize distance in # levels" }
+ "Discretize distance in this number of levels" }
};
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{
if(fflush(fplog) != 0)
{
- gmx_fatal(FARGS,"Cannot flush logfile - maybe you are out of quota?");
+ gmx_fatal(FARGS,"Cannot flush logfile - maybe you are out of disk space?");
}
}
}
{ "-multi", FALSE, etINT,{&nmultisim},
"HIDDENDo multiple simulations in parallel" },
{ "-replex", FALSE, etINT, {&repl_ex_nst},
- "HIDDENAttempt replica exchange every # steps" },
+ "HIDDENAttempt replica exchange periodically with this period (steps)" },
{ "-reseed", FALSE, etINT, {&repl_ex_seed},
"HIDDENSeed for replica exchange, -1 is generate a seed" },
{ "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
t_pargs pa[] = {
{ "-nlevels", FALSE, etINT, {&nlevels},
- "Discretize rms in # levels" },
+ "Discretize RMS in this number of levels" },
{ "-max", FALSE, etREAL, {&scalemax},
"Maximum level in matrices" },
{ "-sumh", FALSE, etBOOL, {&bSumH},
- "average distance over equivalent hydrogens" },
+ "Average distance over equivalent hydrogens" },
{ "-pbc", FALSE, etBOOL, {&bPBC},
"Use periodic boundary conditions when computing distances" }
};
"[TT]g_sorient[tt] analyzes solvent orientation around solutes.",
"It calculates two angles between the vector from one or more",
"reference positions to the first atom of each solvent molecule:[PAR]",
- "[GRK]theta[grk]1: the angle with the vector from the first atom of the solvent",
+ "[GRK]theta[grk][SUB]1[sub]: the angle with the vector from the first atom of the solvent",
"molecule to the midpoint between atoms 2 and 3.[BR]",
- "[GRK]theta[grk]2: the angle with the normal of the solvent plane, defined by the",
+ "[GRK]theta[grk][SUB]2[sub]: the angle with the normal of the solvent plane, defined by the",
"same three atoms, or, when the option [TT]-v23[tt] is set, ",
"the angle with the vector between atoms 2 and 3.[PAR]",
"The reference can be a set of atoms or",
"consist of 3 atoms per solvent molecule.",
"Only solvent molecules between [TT]-rmin[tt] and [TT]-rmax[tt] are",
"considered for [TT]-o[tt] and [TT]-no[tt] each frame.[PAR]",
- "[TT]-o[tt]: distribtion of cos([GRK]theta[grk]1) for rmin<=r<=rmax.[PAR]",
- "[TT]-no[tt]: distribution of cos([GRK]theta[grk]2) for rmin<=r<=rmax.[PAR]",
- "[TT]-ro[tt]: <cos([GRK]theta[grk]1)> and <3cos^2([GRK]theta[grk]2)-1> as a function of the",
+ "[TT]-o[tt]: distribtion of [MATH][COS][GRK]theta[grk][SUB]1[sub][cos][math] for rmin<=r<=rmax.[PAR]",
+ "[TT]-no[tt]: distribution of [MATH][COS][GRK]theta[grk][SUB]2[sub][cos][math] for rmin<=r<=rmax.[PAR]",
+ "[TT]-ro[tt]: [MATH][CHEVRON][COS][GRK]theta[grk][SUB]1[sub][cos][chevron][math] and [MATH][CHEVRON]3[COS]^2[GRK]theta[grk][SUB]2[sub][cos]-1[chevron][math] as a function of the",
"distance.[PAR]",
"[TT]-co[tt]: the sum over all solvent molecules within distance r",
- "of cos([GRK]theta[grk]1) and 3cos^2([GRK]theta[grk]2)-1 as a function of r.[PAR]",
+ "of [MATH][COS][GRK]theta[grk][SUB]1[sub][cos][math] and [MATH]3[COS]^2([GRK]theta[grk][SUB]2[sub])-1[cos][math] as a function of r.[PAR]",
"[TT]-rc[tt]: the distribution of the solvent molecules as a function of r"
};
{ "-multi", FALSE, etINT, {&nmultisim},
"Do multiple simulations in parallel" },
{ "-replex", FALSE, etINT, {&repl_ex_nst},
- "Attempt replica exchange periodically with this period" },
+ "Attempt replica exchange periodically with this period (steps)" },
{ "-reseed", FALSE, etINT, {&repl_ex_seed},
"Seed for replica exchange, -1 is generate a seed" },
{ "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
{ "-hyd", FALSE, etBOOL, {&bH},
"Include angles with atoms with mass < 1.5" },
{ "-hq", FALSE, etREAL, {&hq},
- "Ignore angles with atoms with mass < 1.5 and |q| < hq" }
+ "Ignore angles with atoms with mass < 1.5 and magnitude of their charge less than this value" }
};
output_env_t oenv;
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff