[gmx-users] Problem with G_WHAM and -bsprof command

Justin Lemkul jalemkul at vt.edu
Mon Nov 20 17:12:47 CET 2017

On 11/20/17 10:18 AM, ABEL Stephane wrote:
> hello everybody
> I am trying to obtain the average and SD of PMF profile with gmx wham (gmx 5.1.2 and 2016.1) with the following command in a bash script
> mpirun -np 1 gmx_mpi wham -it Wham_TPR_step5.dat -if Wham_Pullf_step5.dat -unit kCal -temp 298 -b $begin -e $end -hist "$NameFile"_"$Name"_hist.xvg -o "$NameFile"_"$Name"_profile.xvg -bs-method hist -min 0.0 -max 5.6 -bsprof "$NameFile"_"$Name"_profile_bsResult.xvg
> According to the manual, the -bsres  should ouput the "Average profile and standard deviations". The calculations runs with no errors  but I do not obtain "$NameFile"_"$Name"_profile_bsResult.xvg file. Am I missing something.

Probably the fact that -nBootstrap defaults to zero, so you need to 
specify a real value if you want output from bootstrapping.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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