[gmx-users] Problem in Bootstrapping of PMF

Justin Lemkul jalemkul at vt.edu
Tue May 16 16:06:57 CEST 2017

On 5/16/17 7:15 AM, Alex wrote:
> 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
> bsResult.xvg.
> 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.

Does it work if you run normally, e.g. not via mpirun?  There's nothing to gain 
here by doing this.  The latest gmx wham can use OpenMP via the OMP_NUM_THREADS 
environment variable if you want to speed things up.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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