[gmx-users] Doubt about gmx wham analysis

Varvdekar Bhagyesh Rajendra bhagyesh.varvdekar at research.iiit.ac.in
Wed May 31 14:34:19 CEST 2017

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"

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).

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.

Thank you for the help in answering the doubt.

Best Regards,

----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Sent: Wednesday, May 31, 2017 5:42:52 AM
Subject: Re: [gmx-users] Doubt about gmx wham analysis

On 5/30/17 6:49 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear all,
> I have followed the Umbrella sampling tutorial (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html) on a Protein-ligand system using gromacs 5.1.1 while making some changes in md_pull code with pull_coord1_dim = Y Y Y . Now I have to perform WHAM analysis using gmx wham. As my system (Protein-ligand system) has the reaction coordinate as the center of masses between the protein and ligand I have to supply the .pdo file as suggested in gmx wham help menu. I would appreciate if anyone could help me to generate these pdo files because I have not encountered any option to generate them.

.pdo files were umbrella sampling output files from ancient versions of GROMACS. 
  Support for their interpretation is maintained only for backwards compatibility.

Look through the tutorial again; nowhere does it use .pdo files and yet it still 
calculates a PMF :)



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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