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

[ABEL Stephane]

Many thanks Anthony

I will read your post blog. I have another quick question: Does the approach work by defaults (w/o modifications) for other biomolecules such as surfactants or it is necessary to construct a virtual site table as we can found for protein in the charmm*.ff distribution ? 

Stéphane



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Message: 3
Date: Fri, 6 Apr 2018 09:33:46 +0000
From: Anthony Nash <anthony.nash at dpag.ox.ac.uk>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Speed up simulations with GROMACS with
        virtual interaction sites
Message-ID:
        <84462751076E544CBB9E12BCCA3E2D49389DB4 at MBX12.ad.oak.ox.ac.uk>
Content-Type: text/plain; charset="iso-8859-1"


Hi,

I tried something like this about a year ago and I put an instructional blog post together. Warning: it was pulled together from a paper I found and not my own efforts although I did get it to work. Any questions I might not be able to respond, I'm on vacation!

https://distributedscience.wordpress.com/2017/06/19/speeding-up-md-simulations-in-explicit-solvent/

Kind regards
Anthony Nash PhD MRSC
Department of Physiology, Anatomy, and Genetics
University of Oxford
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of ABEL Stephane [Stephane.ABEL at cea.fr]
Sent: 06 April 2018 08:51
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Speed up simulations with GROMACS with virtual     interaction sites

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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