Re: [gmx-users] how to distance between COM of two groups of atoms?
Fixed! 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.
Re: [gmx-users] how to distance between COM of two groups of atoms?
On 7/1/16 8:56 PM, Ming Tang wrote: Thank you Justin, I set 2 groups (start and end )in index.ndx file. each group has 3 alpha carbon atoms. I used the following command to calculate the distance between COM of those 2 groups gmx distance -n index.ndx -select 'com of group "start" plus com of group "end"' -f test.pdb -s topol.tpr -oxyz dist.xvg and got average distance:4.385, which is not correct as my protein is around 30-nm-long. is the command I used correct? The value returned is the shortest periodic distance. Use -nopbc. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] how to distance between COM of two groups of atoms?
Thank you Justin, I set 2 groups (start and end )in index.ndx file. each group has 3 alpha carbon atoms. I used the following command to calculate the distance between COM of those 2 groups gmx distance -n index.ndx -select 'com of group "start" plus com of group "end"' -f test.pdb -s topol.tpr -oxyz dist.xvg and got average distance:4.385, which is not correct as my protein is around 30-nm-long. is the command I used correct? -- 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] how to distance between COM of two groups of atoms?
On 7/1/16 7:29 PM, Ming Tang wrote: Dear list, I found that gmx distance can calculate distance between 2 atoms. is there a way to calculate distance centre of mass between 2 group of atoms? Yes, with gmx distance. For instance: http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0#g_dist -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] how to distance between COM of two groups of atoms?
Dear list, I found that gmx distance can calculate distance between 2 atoms. is there a way to calculate distance centre of mass between 2 group of atoms? Thanks, Ming -- 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.
