[gmx-users] Md simulation trajectory Analysis.

Mark Abraham mark.j.abraham at gmail.com
Mon Nov 14 07:24:39 CET 2016


On Mon, 14 Nov 2016 07:14 maria khan <mariabiochemist1 at gmail.com> wrote:

Dear Justin Lemkul..
Analysing trajectories of Md simulation,,how the H-bonds can be
analysed..if after minimization the software has once ignored the

Typical force fields don't explicitly model hydrogen bonds, but that
doesn't mean the underlying physics is ignored. "Analyse the h-bonds" is a
bit vague. What did you design the simulation to observe?

Secondly how can we rename the H atoms by the gromacs conventional
system.Guide me in renaming H atoms of His residue according to conventions?

Why do you think you need to?


Maria khan
regards and thank.
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