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

[Justin Lemkul]

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

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

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