[gmx-users] Multiple protein simulations in a box

Justin Lemkul jalemkul at vt.edu
Fri Nov 2 11:24:29 CET 2012

On 11/2/12 5:52 AM, Rajeswari A. wrote:
> Dear Gromacs Users,
> I want to simulate multiple number of proteins in a box. I am very confused
> in choosing what MD method will be useful to solve my problem. Can i do it
> with regular molecular dynamics simulations? I am not sure whether
> diffusion of solutes are taken care in standard MD. or should i opt
> brownian dynamics for this purpose? Is there any special method where i can
> do simulate multiple proteins in a box?

You can use standard MD methodology.  Most of the literature I have seen 
involving multiple proteins does.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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