/* create a collection (array) of barres_t object given a ordered linked list
of barlamda_t sample collections */
-static barres_t *barres_list_create(lambda_t *bl_head, int *nres)
+static barres_t *barres_list_create(lambda_t *bl_head, int *nres,
+ gmx_bool use_dhdl)
{
lambda_t *bl;
int nlambda=0;
barres_init(br);
- if (!scprev && !sc)
+ if (use_dhdl)
{
/* we use dhdl */
{
gmx_fatal(FARGS,"Some dhdl files contain only one value (dH/dl), while others \ncontain multiple values (dH/dl and/or Delta H), will not proceed \nbecause of possible inconsistencies.\n");
}
+ }
+ else if (!scprev && !sc)
+ {
+ gmx_fatal(FARGS,"There is no path from lambda=%g -> %g that is covered by foreign lambdas:\ncannot proceed with BAR.\nUse thermodynamic integration of dH/dl by calculating the averages of dH/dl\nwith g_analyze and integrating them.\nAlternatively, use the -extp option if (and only if) the Hamiltonian\ndepends linearly on lambda, which is NOT normally the case.\n", bl->prev->lambda, bl->lambda);
}
/* normal delta H */
if (!scprev)
{
- gmx_fatal(FARGS,"Could not find a set for lambda = %g in the files for lambda = %g",bl->lambda,bl->prev->lambda);
+ gmx_fatal(FARGS,"Could not find a set for foreign lambda = %g\nin the files for lambda = %g",bl->lambda,bl->prev->lambda);
}
if (!sc)
{
- gmx_fatal(FARGS,"Could not find a set for lambda = %g in the files for lambda = %g",bl->prev->lambda,bl->lambda);
+ gmx_fatal(FARGS,"Could not find a set for foreign lambda = %g\nin the files for lambda = %g",bl->prev->lambda,bl->lambda);
}
br->a = scprev;
br->b = sc;
"controlled by a parameter, [GRK]lambda[grk] (see the [TT].mdp[tt] parameter",
"[TT]init_lambda[tt]). The BAR method calculates a ratio of weighted",
"average of the Hamiltonian difference of state B given state A and",
- "vice versa. If the Hamiltonian does not depend linearly on [GRK]lambda[grk]",
- "(in which case we can extrapolate the derivative of the Hamiltonian",
- "with respect to [GRK]lambda[grk], as is the default when [TT]free_energy[tt] is on),",
- "the energy differences to the other state need to be calculated",
- "explicitly during the simulation. This can be controlled with",
+ "vice versa.",
+ "The energy differences to the other state must be calculated",
+ "explicitly during the simulation. This can be done with",
"the [TT].mdp[tt] option [TT]foreign_lambda[tt].[PAR]",
"Input option [TT]-f[tt] expects multiple [TT]dhdl.xvg[tt] files. ",
"Two types of input files are supported:[BR]",
- "[TT]*[tt] Files with only one [IT]y[it]-value, for such files it is assumed ",
- " that the [IT]y[it]-value is dH/d[GRK]lambda[grk] and that the Hamiltonian depends ",
- " linearly on [GRK]lambda[grk]. The [GRK]lambda[grk] value of the simulation is inferred ",
- " from the subtitle (if present), otherwise from a number in the",
- " subdirectory in the file name.",
+ "[TT]*[tt] Files with more than one [IT]y[it]-value. ",
+ "The files should have columns ",
+ "with dH/d[GRK]lambda[grk] and [GRK]Delta[grk][GRK]lambda[grk]. ",
+ "The [GRK]lambda[grk] values are inferred ",
+ "from the legends: [GRK]lambda[grk] of the simulation from the legend of ",
+ "dH/d[GRK]lambda[grk] and the foreign [GRK]lambda[grk] values from the ",
+ "legends of Delta H",
"[BR]",
- "[TT]*[tt] Files with more than one [IT]y[it]-value. The files should have columns ",
- " with dH/d[GRK]lambda[grk] and [GRK]Delta[grk][GRK]lambda[grk]. The [GRK]lambda[grk] values are inferred ",
- " from the legends: [GRK]lambda[grk] of the simulation from the legend of dH/d[GRK]lambda[grk] ",
- " and the foreign [GRK]lambda[grk] values from the legends of Delta H.[PAR]",
- "The [GRK]lambda[grk] of the simulation is parsed from [TT]dhdl.xvg[tt] file's legend ",
- "containing the string 'dH', the foreign [GRK]lambda[grk] values from the legend ",
- "containing the capitalized letters 'D' and 'H'. The temperature ",
- "is parsed from the legend line containing 'T ='.[PAR]",
+ "[TT]*[tt] Files with only one [IT]y[it]-value. Using the",
+ "[TT]-extp[tt] option for these files, it is assumed",
+ "that the [IT]y[it]-value is dH/d[GRK]lambda[grk] and that the ",
+ "Hamiltonian depends linearly on [GRK]lambda[grk]. ",
+ "The [GRK]lambda[grk] value of the simulation is inferred from the ",
+ "subtitle (if present), otherwise from a number in the subdirectory ",
+ "in the file name.[PAR]",
+
+ "The [GRK]lambda[grk] of the simulation is parsed from ",
+ "[TT]dhdl.xvg[tt] file's legend containing the string 'dH', the ",
+ "foreign [GRK]lambda[grk] values from the legend containing the ",
+ "capitalized letters 'D' and 'H'. The temperature is parsed from ",
+ "the legend line containing 'T ='.[PAR]",
"The input option [TT]-g[tt] expects multiple [TT].edr[tt] files. ",
- "These can contain either lists of energy differences (see the",
- "[TT].mdp[tt] option [TT]separate_dhdl_file[tt]), or a series of histograms",
- "(see the [TT].mdp[tt] options [TT]dh_hist_size[tt] and [TT]dh_hist_spacing[tt]).",
- "The temperature and [GRK]lambda[grk] values are automatically deduced from",
- "the [TT]ener.edr[tt] file.[PAR]"
+ "These can contain either lists of energy differences (see the ",
+ "[TT].mdp[tt] option [TT]separate_dhdl_file[tt]), or a series of ",
+ "histograms (see the [TT].mdp[tt] options [TT]dh_hist_size[tt] and ",
+ "[TT]dh_hist_spacing[tt]).", "The temperature and [GRK]lambda[grk] ",
+ "values are automatically deduced from the [TT]ener.edr[tt] file.[PAR]",
+
+ "In addition to the [TT].mdp[tt] option [TT]foreign_lambda[tt], ",
+ "the energy difference can also be extrapolated from the ",
+ "dH/d[GRK]lambda[grk] values. This is done with the[TT]-extp[tt]",
+ "option, which assumes that the system's Hamiltonian depends linearly",
+ "on [GRK]lambda[grk], which is not normally the case.[PAR]",
"The free energy estimates are determined using BAR with bisection, ",
"with the precision of the output set with [TT]-prec[tt]. ",
"over 5 blocks. A range of block numbers for error estimation can ",
"be provided with the options [TT]-nbmin[tt] and [TT]-nbmax[tt].[PAR]",
- "[TT]g_bar[tt] tries to aggregate samples with the same 'native' and 'foreign'",
- "[GRK]lambda[grk] values, but always assumes independent samples. [BB]Note[bb] that",
- "when aggregating energy differences/derivatives with different",
- "sampling intervals, this is almost certainly not correct. Usually",
- "subsequent energies are correlated and different time intervals mean",
- "different degrees of correlation between samples.[PAR]",
+ "[TT]g_bar[tt] tries to aggregate samples with the same 'native' and ",
+ "'foreign' [GRK]lambda[grk] values, but always assumes independent ",
+ "samples. [BB]Note[bb] that when aggregating energy ",
+ "differences/derivatives with different sampling intervals, this is ",
+ "almost certainly not correct. Usually subsequent energies are ",
+ "correlated and different time intervals mean different degrees ",
+ "of correlation between samples.[PAR]",
"The results are split in two parts: the last part contains the final ",
"results in kJ/mol, together with the error estimate for each part ",
static real begin=0,end=-1,temp=-1;
int nd=2,nbmin=5,nbmax=5;
int nbin=100;
+ gmx_bool use_dhdl=FALSE;
gmx_bool calc_s,calc_v;
t_pargs pa[] = {
{ "-b", FALSE, etREAL, {&begin}, "Begin time for BAR" },
{ "-prec", FALSE, etINT, {&nd}, "The number of digits after the decimal point" },
{ "-nbmin", FALSE, etINT, {&nbmin}, "Minimum number of blocks for error estimation" },
{ "-nbmax", FALSE, etINT, {&nbmax}, "Maximum number of blocks for error estimation" },
- { "-nbin", FALSE, etINT, {&nbin}, "Number of bins for histogram output"}
+ { "-nbin", FALSE, etINT, {&nbin}, "Number of bins for histogram output"},
+ { "-extp", FALSE, etBOOL, {&use_dhdl}, "Whether to linearly extrapolate dH/dl values to use as energies"}
};
t_filenm fnm[] = {
}
/* assemble the output structures from the lambdas */
- results=barres_list_create(lb, &nresults);
+ results=barres_list_create(lb, &nresults, use_dhdl);
sum_disc_err=barres_list_max_disc_err(results, nresults);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff