From 878fbf47c5044bbe5e47c069238b2e26e97244e9 Mon Sep 17 00:00:00 2001 From: Sander Pronk Date: Thu, 10 Mar 2011 17:27:26 +0100 Subject: [PATCH] Added documentation for multidir. --- src/kernel/mdrun.c | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/src/kernel/mdrun.c b/src/kernel/mdrun.c index f225db4421..6379a6d85d 100644 --- a/src/kernel/mdrun.c +++ b/src/kernel/mdrun.c @@ -263,18 +263,24 @@ int main(int argc,char *argv[]) "The options [TT]-px[tt] and [TT]-pf[tt] are used for writing pull COM", "coordinates and forces when pulling is selected", "in the [TT].mdp[tt] file.[PAR]", - "With [TT]-multi[tt] multiple systems are simulated in parallel.", - "As many input files are required as the number of systems.", - "The system number is appended to the run input and each output filename,", - "for instance [TT]topol.tpr[tt] becomes [TT]topol0.tpr[tt], [TT]topol1.tpr[tt] etc.", + "With [TT]-multi[tt] or [TT]-multidir[tt], multiple systems can be ", + "simulated in parallel.", + "As many input files/directories are required as the number of systems. ", + "The [TT]-multidir[tt] option takes a list of directories (one for each ", + "system) and runs in each of them, using the input/output file names, ", + "such as specified by e.g. the [TT]-s[tt] option, relative to these ", + "directories.", + "With [TT]-multi[tt], the system number is appended to the run input ", + "and each output filename, for instance [TT]topol.tpr[tt] becomes", + "[TT]topol0.tpr[tt], [TT]topol1.tpr[tt] etc.", "The number of nodes per system is the total number of nodes", "divided by the number of systems.", "One use of this option is for NMR refinement: when distance", "or orientation restraints are present these can be ensemble averaged", "over all the systems.[PAR]", "With [TT]-replex[tt] replica exchange is attempted every given number", - "of steps. The number of replicas is set with the [TT]-multi[tt] option,", - "see above.", + "of steps. The number of replicas is set with the [TT]-multi[tt] or ", + "[TT]-multidir[tt] option, described above.", "All run input files should use a different coupling temperature,", "the order of the files is not important. The random seed is set with", "[TT]-reseed[tt]. The velocities are scaled and neighbor searching", -- 2.11.4.GIT