[gmx-users] Md simulation H-atom trajectory analysis.

Mark Abraham mark.j.abraham at gmail.com
Tue Nov 15 09:19:44 CET 2016


On Tue, 15 Nov 2016 06:26 maria khan <mariabiochemist1 at gmail.com> wrote:

Dear justin
Thanks for your prompt response.
My results are satisfactory.and i managed the H-atoms by _ignh command.but
i just want to learn its solution by conventional system of gromacs also
thats y i am asking.

That sounds like you're not yet clear on what gmx pdb2gmx -ignh does. Do
read gmx pdb2gmx -h. Your choice of force field dictates what hydrogen
atoms are modelled.


>From your answer can i say that H-atoms trajectory can be studied either it
is handle by -Ignh command or conventional system??
Before your answer i was thinking that by solving the h-atoms by _ignh
command i ll not be able to study the H-atom trajectory as the software has
ignord it.
Thanks for your honorable guidance.
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