Hi Sayan,
running it technically may not be so difficult, Amber should be able to
handle a simulation box filled with gas. Using that as a realistic model of
the process you want to study will be way more tricky though. You may need
to experiment with simulation step size and cutoff parameters, think about
how to make a thermostat work if particles dont collide very often and
check if the force field describes such a system properly. You may be
better off just simulating the protein in vacuum instead, a gaseous
environment will just lead to the protein experiencing occasional kicks on
its surface, not unlike a Langevin thermostat would do as well.
Kind Regards,
Thomas
On Tue, Jul 18, 2023 at 12:00 PM Sayan Poddar via AMBER <amber.ambermd.org>
wrote:
> Dear AMBER developers and Users,
>
> Is there any way of running a protein simulation in a gaseous environment
> instead of a solvated (water) environment?
>
> --
> *with regards*
> *Sayan Poddar*
>
> *PhD Research Scholar*
> *Department of Biosciences and Biomedical Engineering*
> *Indian Institute of Technology Indore*
> *India*
> _______________________________________________
> AMBER mailing list
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>
--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Wed Jul 19 2023 - 00:00:02 PDT
