[gmx-users] Distances calculation in umbrella sampling

Amir Zeb zebamir85 at gmail.com
Thu Nov 30 07:58:13 CET 2017

Hello gmx users,

I want to calculate binding free energy for protein-ligand complex by
Umbrella sampling in Gromacs. I have extracted each frame's gro file for
500 frames after pulling simulation. Now, I want to calculate the distances
between the representative gro files by executing the script given by Dr.
Justin in his tutorial. I have replaced the Chain_A by ligand name and
Chain_B by Protein_ZN in original script to represent my index file groups.
The summary_distances.dat file is generating successfully, but it has no
distances information. Only frames number are given on a single column and
is repeated again after 500th frame. The summary_distances.dat file is
attached for your kind consideration.
Please let me know if there is any possibility to fix this issue.

Thanks in advance!

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