[gmx-users] Doubt about gmx wham analysis

Varvdekar Bhagyesh Rajendra bhagyesh.varvdekar at research.iiit.ac.in
Tue May 30 12:49:16 CEST 2017

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.

Thanking in anticipation,
IIIT Hyderabad, India

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