Re: [gmx-users] Speed up simulations with GROMACS with virtual interaction sites
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.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 6 Apr 2018, at 13:11, Anthony Nash <anthony.n...@dpag.ox.ac.uk<mailto:anthony.n...@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-boun...@maillist.sys.kth.se<mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se> [gromacs.org_gmx-users-boun...@maillist.sys.kth.se<mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se>] on behalf of ABEL Stephane [stephane.a...@cea.fr<mailto:stephane.a...@cea.fr>] Sent: 06 April 2018 11:20 To: gromacs.org_gmx-users@maillist.sys.kth.se<mailto:gromacs.org_gmx-users@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 + From: Anthony Nash <anthony.n...@dpag.ox.ac.uk<mailto:anthony.n...@dpag.ox.ac.uk>> To: "gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>" <gmx-us...@gromacs.org<mailto: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<mailto: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. -- 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.
[gmx-users] Speed up simulations with GROMACS with virtual interaction sites
I know the paper but the webpage Thanks you Viveca -- Message: 2 Date: Fri, 6 Apr 2018 16:45:45 +0200 From: Viveca Lindahl <vivecalind...@gmail.com> To: gmx-us...@gromacs.org Cc: "gromacs.org_gmx-users@maillist.sys.kth.se" <gromacs.org_gmx-users@maillist.sys.kth.se> Subject: Re: [gmx-users] Speed up simulations with GROMACS with virtual interaction sites Message-ID:
Re: [gmx-users] Speed up simulations with GROMACS with virtual interaction sites
Hi, There is this ancient gromacs page which I guess you already found: http://www.gromacs.org/Documentation/How-tos/Removing_fastest_degrees_of_freedom 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). -- Viveca On Fri, Apr 6, 2018 at 9:51 AM, ABEL Stephanewrote: > 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 > > Stéphane > > -- > 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.
Re: [gmx-users] Speed up simulations with GROMACS with virtual interaction sites
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-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 11:20 To: gromacs.org_gmx-users@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 + 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. -- 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.
[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 + 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.
Re: [gmx-users] Speed up simulations with GROMACS with virtual interaction sites
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 Stéphane -- 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.
[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 Stéphane -- 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.