[gmx-users] Md simulation trajectory Analysis.

[Mark Abraham]

Hi,

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
H-bonds..??


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?

Mark

Maria khan
regards and thank.
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