[gmx-users] Doubt about gmx wham analysis

Justin Lemkul jalemkul at vt.edu
Wed May 31 02:13:01 CEST 2017

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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