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 ------------------------------ Message: 3 Date: Fri, 6 Apr 2018 09:33:46 +0000 From: Anthony Nash <anthony.n...@dpag.ox.ac.uk> To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> Subject: Re: [gmx-users] Speed up simulations with GROMACS with virtual interaction sites Message-ID: <84462751076e544cbb9e12bcca3e2d49389...@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-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of ABEL Stephane [stephane.a...@cea.fr] Sent: 06 April 2018 08:51 To: gromacs.org_gmx-users@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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. ------------------------------ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. End of gromacs.org_gmx-users Digest, Vol 168, Issue 24 ****************************************************** -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.