[gmx-users] Problem in Bootstrapping of PMF

Alex alexanderwien2k at gmail.com
Tue May 16 13:16:40 CEST 2017

Hello gromacs user,

I have calculated the PMF by umbrella sampling for my system, by below
command I am trying to Bootstrap my PMF, but I do not know why bsResult.xvg
in whcih the error bars is stored can not be produced. The rests contain
Profile, bsProfs.xvg are easily be calculated though.

I increased the time and number of used 512 CPU's, but after more than one
week the bootstrapping stopped again just because of time limit with out

I have already done nicely the same calculation for some similar systems,
even with higher number of bins and bootstraps, and this is the only one I
have problem with in spite of the similar ingredients.

#$ -l h_rt=850000,h_vmem=3200M
#$ -notify
#$ -cwd
#$ -A gromacs_parallel
#$ -pe orte_sl16* 512

        mpirun -x PATH -np 1 gmx_mpi wham -hist Histo.xvg -nBootstrap 350
-bins 350 -bs-method b-hist -bsres bsResult.xvg -bsprof bsProfs.xvg -if
Fpull.dat -it TPR.dat -min 1.18 -max 3.6 -ac -o Profile.xvg -zprof0 3.6 -b
48000 -unit kCal >bot.log 2>&1

An help is highly appreciated.


More information about the gromacs.org_gmx-users mailing list