Hi,
You will want to run in the NVE ensemble (i.e. ntp=0, ntt=0) so you
don't have effects from barostat/thermostat and make your timestep 1
fs maximum. You could also run with a weak-coupling thermostat
(Berendsen, ntt=1) with a very long coupling time. As an example, see
http://pubs.acs.org/doi/abs/10.1021/jp0761564.
Hope this helps,
-Dan
On Sun, Dec 14, 2014 at 8:39 AM, Robin Jain <robinjain.chem.gmail.com> wrote:
> Dear all,
> I have equilibrated a organic molecule in 2048 methanol molecule in NPT
> ensemble. Now i want to calculate diffusion constant,so what must be the
> methodology for further MD run and what must be the input file for that.
> Please help me in this regard.
> Thanking You in advance.
> --
> Robin Jain
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sun Dec 14 2014 - 09:00:02 PST
