[gmx-users] Speed up simulations with GROMACS with virtual interaction sites

ABEL Stephane Stephane.ABEL at cea.fr
Fri Apr 6 17:29:05 CEST 2018

I know the paper but the webpage

Thanks you Viveca 


Message: 2
Date: Fri, 6 Apr 2018 16:45:45 +0200
From: Viveca Lindahl <vivecalindahl at gmail.com>
To: gmx-users at gromacs.org
Cc: "gromacs.org_gmx-users at maillist.sys.kth.se"
        <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] Speed up simulations with GROMACS with
        virtual interaction sites
        <CABxAduWJh4VDyNpeVu0nzd9dZSx3rVgX=z_4yXnsQ04AMQMkNQ at mail.gmail.com>
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There is this ancient gromacs page which I guess you already found:

Here are a couple of references, the second for using virtual sites for
CHARMM lipids:

Bjelkmar, P., Larsson, P., Cuendet, M. A., Hess, B. & Lindahl, E.
Implementation of the CHARMM force field in GROMACS: Analysis of protein
stability effects from correction maps, virtual interaction sites, and
water models. Journal of Chemical Theory and Computation 6, 459?466 (2010).
Loubet, B., Kopec, W. & Khandelia, H. Accelerating all-atom MD simulations
of lipids using a modified virtual-sites technique. Journal of Chemical
Theory and Computation 10, 5690?5695 (2014).


On Fri, Apr 6, 2018 at 9:51 AM, ABEL Stephane <Stephane.ABEL at cea.fr> wrote:

> Hi gmx users,
> I know that it is possible to speed up  the simulations by a factor 2 (by
> using a larger timestep) in GROMACS with virtual interaction sites. By I do
> not find a clear procedure on the web in particular if I use CHARMM. Do you
> have any pointers or procedures and examples of mdp files to share with me
> Thanks
> St?phane
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