Re: [gmx-users] How to fix protein went out water?
On 6/17/14, 7:56 AM, Batdorj Batsaikhan wrote: Dear gmx_users, I am working on simulation of protein in water. 10 ns after the protein went out from water. How to fix this? Can I continue my simulation? http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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 fix protein went out water?
Hi Batsaikhan You should re-do the simulation, perfoming it within a box of water with PBC (you can do this with the editconf) Kind regards Thales 2014-06-17 8:56 GMT-03:00 Batdorj Batsaikhan batsaikhan...@yahoo.com: Dear gmx_users, I am working on simulation of protein in water. 10 ns after the protein went out from water. How to fix this? Can I continue my simulation? Best regards, Batsaikhan -- 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] How to fix protein went out water?
On 6/17/14, 10:54 AM, Thales Kronenberger wrote: Hi Batsaikhan You should re-do the simulation, perfoming it within a box of water with PBC (you can do this with the editconf) There is no need to re-do anything. PBC means it is totally irrelevant whether the protein is conveniently centered in the box or not; the forces are the same. The protein drifting outside the box is a total non-issue, since there is no such thing as outside of a periodic system. All one needs to do is apply trjconv for convenient visualization, and no action needs to be taken to continue the run; mdrun doesn't care about our conventions for watching the trajectory. -Justin Kind regards Thales 2014-06-17 8:56 GMT-03:00 Batdorj Batsaikhan batsaikhan...@yahoo.com: Dear gmx_users, I am working on simulation of protein in water. 10 ns after the protein went out from water. How to fix this? Can I continue my simulation? Best regards, Batsaikhan -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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 fix protein went out water?
Thank you Justin and Thales. Best regards, Batsaikhan On Tuesday, June 17, 2014 11:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/17/14, 10:54 AM, Thales Kronenberger wrote: Hi Batsaikhan You should re-do the simulation, perfoming it within a box of water with PBC (you can do this with the editconf) There is no need to re-do anything. PBC means it is totally irrelevant whether the protein is conveniently centered in the box or not; the forces are the same. The protein drifting outside the box is a total non-issue, since there is no such thing as outside of a periodic system. All one needs to do is apply trjconv for convenient visualization, and no action needs to be taken to continue the run; mdrun doesn't care about our conventions for watching the trajectory. -Justin Kind regards Thales 2014-06-17 8:56 GMT-03:00 Batdorj Batsaikhan batsaikhan...@yahoo.com: Dear gmx_users, I am working on simulation of protein in water. 10 ns after the protein went out from water. How to fix this? Can I continue my simulation? Best regards, Batsaikhan -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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. -- 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.
