[gmx-users] Doubt about gmx wham analysis

abhisek Mondal abhisek.mndl at gmail.com
Wed May 31 08:33:03 CEST 2017

On Tue, May 30, 2017 at 4:19 PM, Varvdekar Bhagyesh Rajendra <
bhagyesh.varvdekar at research.iiit.ac.in> 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.
> Hi,

    pullf/x files do the trick in newer versions. pdo files are an ancient
concept, if I got it correctly.
Read here: https://linux.die.net/man/1/g_wham


> Thanking in anticipation,
> Bhagyesh
> IIIT Hyderabad, India
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Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*


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