[gmx-users] Doubt about gmx wham analysis
Varvdekar Bhagyesh Rajendra
bhagyesh.varvdekar at research.iiit.ac.in
Wed May 31 15:21:17 CEST 2017
Many Thanks for the swift reply and the help in answering my doubts.
----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Sent: Wednesday, May 31, 2017 6:06:59 PM
Subject: Re: [gmx-users] Doubt about gmx wham analysis
On 5/31/17 8:34 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
> In my Protein-ligand system, I have used pull_coord1_dim = Y Y Y and the ligand is pulled along the COM of two groups protein-ligand in all directions to calculate binding affinity using umbrella sampling. On the other hand, the tutorials use pull_coord1_dim = N N Y. Hence, I concluded my reaction coordinate differs as mentioned in the help menu of gmx wham : "If you have some unusual reaction coordinate you may also generate your own .pdo files and feed them with the -ip option into to gmx wham"
The fact that your reaction coordinate is different from the tutorial is
irrelevant. You have an absolutely normal reaction coordinate and does not
apply to what the gmx wham help text is talking about (which is probably a very
outdated note at this point, given the massive changes in the pull code in
> Also, the following warning is thrown by gmx wham: " WARNING, no data point in bin 7 (z=0.403502) ! You may not get a reasonable profile. Check your histograms! "
> I was not sure if the z corresponds to the coordinate axis or just the z-axis (which was not the only reaction coordinate in my system).
It is the length along zeta, the reaction coordinate. Don't confuse it with the
z-axis, it's just shorthand.
> All this made me conclude that the pullx files are not enough and the so called pdo files must be necessary, hence the doubt arised. I would appreciate if some more light is shed in this area.
You need better sampling, not archaic file formats.
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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