[gmx-users] Distances calculation in umbrella sampling

[Rose]

Till nowi think the only solution is to use gmx distance for each conf.gro files.then use perl script.
don't forget to delete gmx distance line from script.

-Rose

Sent from my iPhone

> On Nov 30, 2017, at 10:28, Amir Zeb <zebamir85 at gmail.com> wrote:
> 
> 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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