Re: [gmx-users] fix COM of a group
Dear Tsjerk, Yes, you are right. I want to fix the COM of the reference group (one end of a triple helix), and pull the other end. I tried to freeze the reference group, but found this setting restricted the unfolding process of my triple helix. That's why I want to find a way to fix the COM only. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Wednesday, 3 June 2015 11:18 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] fix COM of a group Hi Ming Tang, You didn't tell you were pulling... That's a totally different matter. I guess you want to use two pull groups and pull one with respect to the other. Cheers, Tsjerk On Wed, Jun 3, 2015 at 11:20 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear Tsjerk, Thanks for your guidance. I add those two command lines you gave in .mdp, but got the following warnings. WARNING 1 [file dynamic.mdp]: Some atoms are not part of any center of mass motion removal group. This may lead to artifacts. In most cases one should use one group for the whole system. Number of degrees of freedom in T-Coupling group Protein is 8680.88 Number of degrees of freedom in T-Coupling group non-Protein is 202734.12 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K Calculated rlist for 1x1 atom pair-list as 1.406 nm, buffer size 0.006 nm Set rlist, assuming 4x4 atom pair-list, to 1.400 nm, buffer size 0.000 nm WARNING 2 [file dynamic.mdp]: You are using an absolute reference for pulling, but the rest of the system does not have an absolute reference. This will lead to artifacts. Pull group natoms pbc atom distance at start reference at t=0 0 0 0 1 3 1919 -1.542 nm -1.542 nm Can I just ignore them? Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Wednesday, 3 June 2015 5:41 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] fix COM of a group Hi Ming Tang, comm_mode = Linear comm_grps = CA Cheers, Tsjerk On Wed, Jun 3, 2015 at 9:34 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear all, Is there any method that can fix the center of mass of a group of atoms? I create a group containing CA atoms of the first residue in each of the three chains, and want to fix its center of mass only without freeze the CA atoms. Thanks. -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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] fix COM of a group
Dear Tsjerk, Thanks for your guidance. I add those two command lines you gave in .mdp, but got the following warnings. WARNING 1 [file dynamic.mdp]: Some atoms are not part of any center of mass motion removal group. This may lead to artifacts. In most cases one should use one group for the whole system. Number of degrees of freedom in T-Coupling group Protein is 8680.88 Number of degrees of freedom in T-Coupling group non-Protein is 202734.12 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K Calculated rlist for 1x1 atom pair-list as 1.406 nm, buffer size 0.006 nm Set rlist, assuming 4x4 atom pair-list, to 1.400 nm, buffer size 0.000 nm WARNING 2 [file dynamic.mdp]: You are using an absolute reference for pulling, but the rest of the system does not have an absolute reference. This will lead to artifacts. Pull group natoms pbc atom distance at start reference at t=0 0 0 0 1 3 1919 -1.542 nm -1.542 nm Can I just ignore them? Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Wednesday, 3 June 2015 5:41 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] fix COM of a group Hi Ming Tang, comm_mode = Linear comm_grps = CA Cheers, Tsjerk On Wed, Jun 3, 2015 at 9:34 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear all, Is there any method that can fix the center of mass of a group of atoms? I create a group containing CA atoms of the first residue in each of the three chains, and want to fix its center of mass only without freeze the CA atoms. Thanks. -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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] fix COM of a group
Hi Ming Tang, comm_mode = Linear comm_grps = CA Cheers, Tsjerk On Wed, Jun 3, 2015 at 9:34 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear all, Is there any method that can fix the center of mass of a group of atoms? I create a group containing CA atoms of the first residue in each of the three chains, and want to fix its center of mass only without freeze the CA atoms. Thanks. -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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] fix COM of a group
Hi Ming Tang, You didn't tell you were pulling... That's a totally different matter. I guess you want to use two pull groups and pull one with respect to the other. Cheers, Tsjerk On Wed, Jun 3, 2015 at 11:20 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear Tsjerk, Thanks for your guidance. I add those two command lines you gave in .mdp, but got the following warnings. WARNING 1 [file dynamic.mdp]: Some atoms are not part of any center of mass motion removal group. This may lead to artifacts. In most cases one should use one group for the whole system. Number of degrees of freedom in T-Coupling group Protein is 8680.88 Number of degrees of freedom in T-Coupling group non-Protein is 202734.12 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K Calculated rlist for 1x1 atom pair-list as 1.406 nm, buffer size 0.006 nm Set rlist, assuming 4x4 atom pair-list, to 1.400 nm, buffer size 0.000 nm WARNING 2 [file dynamic.mdp]: You are using an absolute reference for pulling, but the rest of the system does not have an absolute reference. This will lead to artifacts. Pull group natoms pbc atom distance at start reference at t=0 0 0 0 1 3 1919 -1.542 nm -1.542 nm Can I just ignore them? Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Wednesday, 3 June 2015 5:41 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] fix COM of a group Hi Ming Tang, comm_mode = Linear comm_grps = CA Cheers, Tsjerk On Wed, Jun 3, 2015 at 9:34 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear all, Is there any method that can fix the center of mass of a group of atoms? I create a group containing CA atoms of the first residue in each of the three chains, and want to fix its center of mass only without freeze the CA atoms. Thanks. -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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.
