Re: [gmx-users] genion command
On 5/16/17 12:55 AM, Saumyak Mukherjee wrote: Hello Diana, You may try using the -conc flag in genion program to specify your salt concentration, along with -nname and -pname flags. The -nname and -pname options are irrelevant here. If there are fewer than 1000 waters in the system, I doubt the number of ions has been calculated correctly, though. Compare with -conc 0.6 to see if the math is right, and make sure that the solvent is actually being replaced, not anything else. -Justin Best wishes, Saumyak On 16 May 2017 at 10:18, diana p wrote: Dear gmx users, I want to simulate 0.6M CaCL2 aqueous solution. To add the ions I use genion command and add 720 CL and 360 Ca ions respectively to the system of pure 12568 water molecules.But on running the command genion I get error message: Program genion, VERSION 4.6.5 Source code file: /build/buildd/gromacs-4.6.5/src/tools/gmx_genion.c, line: 89 Fatal error: No more replaceable solvent! How should I add ions in the system.I would be more than pleased if someone could guid me. Thank You in advance -- 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 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] genion command
Hello Diana, You may try using the -conc flag in genion program to specify your salt concentration, along with -nname and -pname flags. Best wishes, Saumyak On 16 May 2017 at 10:18, diana p wrote: > Dear gmx users, > I want to simulate 0.6M CaCL2 aqueous solution. To add the ions I use > genion command and add 720 CL and 360 Ca ions respectively to the system of > pure 12568 water molecules.But on running the command genion I get error > message: > > Program genion, VERSION 4.6.5 > Source code file: /build/buildd/gromacs-4.6.5/src/tools/gmx_genion.c, > line: > 89 > Fatal error: > No more replaceable solvent! > > How should I add ions in the system.I would be more than pleased if someone > could guid me. > Thank You in advance > -- > 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. > -- *Saumyak Mukherjee* Junior Research Fellow Prof. Biman Bagchi's Group Solid State and Structural Chemistry Unit Indian Institute of Science Bangalore - 560012 Mob : 8017292426 Alternative e-mail : saumyakmukher...@gmail.com smukher...@sscu.iisc.ernet.in -- 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] genion command
Dear gmx users, I want to simulate 0.6M CaCL2 aqueous solution. To add the ions I use genion command and add 720 CL and 360 Ca ions respectively to the system of pure 12568 water molecules.But on running the command genion I get error message: Program genion, VERSION 4.6.5 Source code file: /build/buildd/gromacs-4.6.5/src/tools/gmx_genion.c, line: 89 Fatal error: No more replaceable solvent! How should I add ions in the system.I would be more than pleased if someone could guid me. Thank You in advance -- 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] Genion command not working
Thank you very much your reply its working fine if i decrease distance thank you -- View this message in context: http://gromacs.5086.x6.nabble.com/Genion-command-not-working-tp5010776p5014007.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Genion command not working
Hi Srinivas, Have you tried my suggestion? Cheers, Tsjerk On Fri, Jan 24, 2014 at 7:45 AM, srinivasa rao lanke wrote: > IS IT this problem solved or not??? > > > I am also pacing same problem. > > > > > > srinivas > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Genion-command-not-working-tp5010776p5013999.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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] Genion command not working
IS IT this problem solved or not??? I am also pacing same problem. srinivas -- View this message in context: http://gromacs.5086.x6.nabble.com/Genion-command-not-working-tp5010776p5013999.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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.