[gmx-users] Umbrella_pull_simulation

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 15 12:30:54 CET 2012

shahid nayeem wrote:
> The similar files for wt can be assesed at
>  http://www.freefilehosting.net/umbrellawt 
>  I expected wild type binding energy to be less than mutant
> The command used for g_wham is
>  g_wham_mpi_4.5.4  -it tpr-files.dat -if pullf-files.dat -o 
> profile_mut.xvg -hist histo_mut.xvg -unit kCal -b 500 -nBootstrap 200 
> -bsres bsResult_mut.xvg -bsprof bsprofile_mut.xvg  -ac
> I get the values exactly opposite to my expectation and unable to find 
> out where I am wrong please suggest.

Determining flaws in one's model or improved ways of doing things is the hardest 
part about being a scientist.  From the data presented, Gromacs has done its job 
and the results are reasonable.  The fact that they don't align with 
expectations is something you will have to reconcile and only you are equipped 
to deal with it.  No one on this list really knows enough about what you're 
doing to do your thinking for you, nor should they.  The principal function of 
this list is to troubleshoot problems with Gromacs, of which there are none here.

Good luck.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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