Re: [gmx-users] use of -t nvt.cpt option in NPT equilibration
Hi Ansuman, With -t nvt.cpt the positions, velocities and other state information is taken from the .cpt file. Otherwise, the positions and velocities are taken from the lower precision .gro file, and other state information is not available. Adding -t nvt.cpt will result in a more exact continuation, which is of no importance at all if you're still in the equilibration phase. For exact continuation of production runs you'll need to use the .cpt file. Cheers, Tsjerk On Tue, Sep 9, 2014 at 10:38 PM, Ansuman Biswas ansu...@physics.iisc.ernet.in wrote: Hi, Can someone please explain if it is necessary to use the -t flag during NPT equilibration? The following command is mentioned in the lysozyme tutorial: $ grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr whereas , I have found the command without the -t flag in another tutorial: grompp -v -f npt.mdp -c protein-NVT.gro -p protein.top -o protein-NPT.tpr Thanking in advance, regards, ansuman -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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] use of -t nvt.cpt option in NPT equilibration
Hi Ansuman, That is optional. Regards, Vijayan.R On Tue, Sep 9, 2014 at 4:38 PM, Ansuman Biswas ansu...@physics.iisc.ernet.in wrote: Hi, Can someone please explain if it is necessary to use the -t flag during NPT equilibration? The following command is mentioned in the lysozyme tutorial: $ grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr whereas , I have found the command without the -t flag in another tutorial: grompp -v -f npt.mdp -c protein-NVT.gro -p protein.top -o protein-NPT.tpr Thanking in advance, regards, ansuman -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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] use of -t nvt.cpt option in NPT equilibration
On 9/9/14 5:09 PM, R.S.K.Vijayan wrote: Hi Ansuman, That is optional. Generally speaking, no, it's not. The real truth lies in what the .mdp settings are and what the intent of NPT is. If you don't pass the .cpt file to grompp -t, you stand to lose much (or all) of the previous state information, thus introducing discontinuities. Rule of thumb: preserve the previous ensemble unless you have a very good reason to ignore or re-create it. -Justin Regards, Vijayan.R On Tue, Sep 9, 2014 at 4:38 PM, Ansuman Biswas ansu...@physics.iisc.ernet.in wrote: Hi, Can someone please explain if it is necessary to use the -t flag during NPT equilibration? The following command is mentioned in the lysozyme tutorial: $ grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr whereas , I have found the command without the -t flag in another tutorial: grompp -v -f npt.mdp -c protein-NVT.gro -p protein.top -o protein-NPT.tpr Thanking in advance, regards, ansuman -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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.
