[gmx-users] Lipids and virtual site in 4.6.1
Dear GROMACS user, Last week I was watching the GTC talk from Eric Lindahl, and I noticed his insistence on virtual site to accelerate simulation (up to 5ps time step). As a matter of fact our group recently tried to use virtual site on CHARMM36 POPC bilayer and the result where less than stellar. We first did a simulation of a POPC bilayer comparing area per lipid with and without virtual site using GROMACS 4.5.5. We obtained an area per lipid around 0.62 nm^2 per lipid with no virtual site but with virtual site we obtained an area per lipid of more than 0.7 nm^2. After that we found that there was a bug report for the virial calculation with virtual site in version 4.5: http://redmine.gromacs.org/issues/908 The issue being marked as resolved for 4.6 and we tried our hand at both the beta3 and 4.6.1 version of it. The result where better but not perfect: we get 0.65~0.66 nm^2 per lipid. The problem here is that in order to increase the time step we need all hydrogen to be virtual sites, so this include the lipids hydrogen and not just the protein. However if the area per lipid is wrong the stress profile is likely to be changed, which will affect transmembrane proteins. So we do not feel confident about using virtual sites in our lipid simulation. I signal it here because there is a possibility that this is still a bug, If somebody could confirm/infirm that it would be nice. Best, Bastien -- View this message in context: http://gromacs.5086.n6.nabble.com/Lipids-and-virtual-site-in-4-6-1-tp5007063.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Lipids and virtual site in 4.6.1
On 2013-04-08 11:34, Bastien Loubet wrote: Dear GROMACS user, Last week I was watching the GTC talk from Eric Lindahl, and I noticed his insistence on virtual site to accelerate simulation (up to 5ps time step). As a matter of fact our group recently tried to use virtual site on CHARMM36 POPC bilayer and the result where less than stellar. We first did a simulation of a POPC bilayer comparing area per lipid with and without virtual site using GROMACS 4.5.5. We obtained an area per lipid around 0.62 nm^2 per lipid with no virtual site but with virtual site we obtained an area per lipid of more than 0.7 nm^2. After that we found that there was a bug report for the virial calculation with virtual site in version 4.5: http://redmine.gromacs.org/issues/908 The issue being marked as resolved for 4.6 and we tried our hand at both the beta3 and 4.6.1 version of it. The result where better but not perfect: we get 0.65~0.66 nm^2 per lipid. The problem here is that in order to increase the time step we need all hydrogen to be virtual sites, so this include the lipids hydrogen and not just the protein. However if the area per lipid is wrong the stress profile is likely to be changed, which will affect transmembrane proteins. So we do not feel confident about using virtual sites in our lipid simulation. I signal it here because there is a possibility that this is still a bug, If somebody could confirm/infirm that it would be nice. Did you also try to use vsites without increasing the time step, in order to rule out that this is a time step effect rather than a vsite effect? Best, Bastien -- View this message in context: http://gromacs.5086.n6.nabble.com/Lipids-and-virtual-site-in-4-6-1-tp5007063.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Lipids and virtual site in 4.6.1
On 2013-04-08 11:52, David van der Spoel wrote: On 2013-04-08 11:34, Bastien Loubet wrote: Dear GROMACS user, Last week I was watching the GTC talk from Eric Lindahl, and I noticed his insistence on virtual site to accelerate simulation (up to 5ps time step). As a matter of fact our group recently tried to use virtual site on CHARMM36 POPC bilayer and the result where less than stellar. We first did a simulation of a POPC bilayer comparing area per lipid with and without virtual site using GROMACS 4.5.5. We obtained an area per lipid around 0.62 nm^2 per lipid with no virtual site but with virtual site we obtained an area per lipid of more than 0.7 nm^2. After that we found that there was a bug report for the virial calculation with virtual site in version 4.5: http://redmine.gromacs.org/issues/908 The issue being marked as resolved for 4.6 and we tried our hand at both the beta3 and 4.6.1 version of it. The result where better but not perfect: we get 0.65~0.66 nm^2 per lipid. The problem here is that in order to increase the time step we need all hydrogen to be virtual sites, so this include the lipids hydrogen and not just the protein. However if the area per lipid is wrong the stress profile is likely to be changed, which will affect transmembrane proteins. So we do not feel confident about using virtual sites in our lipid simulation. I signal it here because there is a possibility that this is still a bug, If somebody could confirm/infirm that it would be nice. Did you also try to use vsites without increasing the time step, in order to rule out that this is a time step effect rather than a vsite effect? And by the way, you are welcome to reopen the redmine issue and upload file demonstrating the problem. Best, Bastien -- View this message in context: http://gromacs.5086.n6.nabble.com/Lipids-and-virtual-site-in-4-6-1-tp5007063.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
