Thank you David,
Does MM simulation depend on the force field which I used? Because QM calculation depends on the force field which I used and according to that I used amber force field I asked it here. Indeed I was thinking that amber tools can do it for me.
Mohammad.
On Saturday, April 2, 2016 7:26 PM, David A Case <david.case.rutgers.edu> wrote:
On Sat, Apr 02, 2016, mohammad r wrote:
>
> I generated the initial structure of my water-peptide system(the
> topology and coordinate files) by amber tools but I want to do the
> rest ofsimulation in gromacs. Now I want to do QM calculation and
> according to that itdepends on which force fields I used, I don’t
> know that I should do it beforeconversion to gromacs format or
> after conversion? Should I do it onwater-peptide system or just the
> peptide? And are the topology and coordinatefiles sufficient for doing
> this or another files are necessary?
These mostly sound like gromacs questions to me. I certainly suggest running
at least a short pure-MM simulation in gromacs (no QM) first, to make sure
that the force field conversion has gone OK.
...dac
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Received on Sun Apr 03 2016 - 04:00:03 PDT
