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

[Erik Marklund]

Hi,

We are working on a tool for automatic vsite parameter generation, which works with most force fields including CHARMM. Stay tuned.

Kind regards,
Erik
______________________________________________
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>

On 6 Apr 2018, at 13:11, Anthony Nash <anthony.nash at dpag.ox.ac.uk<mailto:anthony.nash at dpag.ox.ac.uk>> wrote:

Hi Stephane,

I hope it is useful. I am afraid I have very little charmm experience. I used the approach posted for an amber ff.   I hope someone can help with the charmm aspect.

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<mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se> [gromacs.org_gmx-users-bounces at maillist.sys.kth.se<mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se>] on behalf of ABEL Stephane [Stephane.ABEL at cea.fr<mailto:Stephane.ABEL at cea.fr>]
Sent: 06 April 2018 11:20
To: gromacs.org_gmx-users at maillist.sys.kth.se<mailto:gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] Speed up simulations with GROMACS with virtual     interaction sites

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.nash at dpag.ox.ac.uk<mailto:anthony.nash at dpag.ox.ac.uk>>
To: "gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>" <gmx-users at gromacs.org<mailto: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<mailto: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

--
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-request at 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-request at 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-request at 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-request at gromacs.org.