Re: [gmx-users] How to extend simulation?
On 4/3/17 2:20 PM, ZHANG Cheng wrote: Thank you. So if the below is correct, and it will run for 100 ns? convert-tpr -s previous.tpr -extend 10 -o next.tpr gmx mdrun -deffnm next -cpi previous.cpt Have you tried it? -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 extend simulation?
Thank you. So if the below is correct, and it will run for 100 ns? convert-tpr -s previous.tpr -extend 10 -o next.tpr gmx mdrun -deffnm next -cpi previous.cpt -- Original -- From: "Justin Lemkul";<jalem...@vt.edu>; Date: Tue, Apr 4, 2017 02:12 AM To: "gmx-users"<gmx-us...@gromacs.org>; Subject: Re: [gmx-users] How to extend simulation? On 4/3/17 2:07 PM, ZHANG Cheng wrote: > (Following Justin's suggestion) > > > Dear Gromacs Researchers, > My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to > extend it to 100 ns. > > > As shown on > http://www.gromacs.org/Documentation/How-tos/Extending_Simulations > > > Should I use the following two lines of code for the files in the same folder? > If the "deffnm" is set correctly? > But in this case, will the new simulation still only have 10 ns? > No. > > convert-tpr -s previous.tpr -extend timetoextendby -o next.tpr If you replace "timetoextendby" with some sensible value of time (ps), then this means "next.tpr" will specify some longer amount of time to run. > gmx mdrun -deffnm next -cpi previous.cpt ...which is then passed to mdrun here. This says "run the longer simulation specified in next.tpr, but start from the point specified in previous.cpt rather than starting over from time zero." -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. -- 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 extend simulation?
On 4/3/17 2:07 PM, ZHANG Cheng wrote: (Following Justin's suggestion) Dear Gromacs Researchers, My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to extend it to 100 ns. As shown on http://www.gromacs.org/Documentation/How-tos/Extending_Simulations Should I use the following two lines of code for the files in the same folder? If the "deffnm" is set correctly? But in this case, will the new simulation still only have 10 ns? No. convert-tpr -s previous.tpr -extend timetoextendby -o next.tpr If you replace "timetoextendby" with some sensible value of time (ps), then this means "next.tpr" will specify some longer amount of time to run. gmx mdrun -deffnm next -cpi previous.cpt ...which is then passed to mdrun here. This says "run the longer simulation specified in next.tpr, but start from the point specified in previous.cpt rather than starting over from time zero." -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 extend simulation?
Hi, Back up your files and try it :-) You will see that mdrun refuses to append if you change -deffnm. So either don't append or don't change the name. Mark On Mon, Apr 3, 2017 at 8:09 PM ZHANG Cheng <272699...@qq.com> wrote: > (Following Justin's suggestion) > > > Dear Gromacs Researchers, > My old.mdp only sets 10 ns of simulation. Now it has finished, and I want > to extend it to 100 ns. > > > As shown on > http://www.gromacs.org/Documentation/How-tos/Extending_Simulations > > > Should I use the following two lines of code for the files in the same > folder? > If the "deffnm" is set correctly? > But in this case, will the new simulation still only have 10 ns? > > > convert-tpr -s previous.tpr -extend timetoextendby -o next.tpr > gmx mdrun -deffnm next -cpi previous.cpt > > > > Thank you. > > > Yours sincerely > Cheng > -- > 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.
[gmx-users] How to extend simulation?
(Following Justin's suggestion) Dear Gromacs Researchers, My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to extend it to 100 ns. As shown on http://www.gromacs.org/Documentation/How-tos/Extending_Simulations Should I use the following two lines of code for the files in the same folder? If the "deffnm" is set correctly? But in this case, will the new simulation still only have 10 ns? convert-tpr -s previous.tpr -extend timetoextendby -o next.tpr gmx mdrun -deffnm next -cpi previous.cpt Thank you. Yours sincerely Cheng -- 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 extend simulation by changing the mdp file?
On 4/3/17 1:41 PM, ZHANG Cheng wrote: Dear Gromacs Researchers, My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to extend it to 100 ns. As shown on http://www.gromacs.org/Documentation/How-tos/Extending_Simulations Should I use the following two lines of code for the files in the same folder? grompp -f new.mdp -c old.tpr -o new.tpr -t old.cpt gmx mdrun -deffnm new -cpi -append You only need to invoke grompp if you're changing output settings and starting a new run, in which case you would not be using -cpi -append in your mdrun command. The use of convert-tpr followed by mdrun is cleaner and easier. -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.
[gmx-users] How to extend simulation by changing the mdp file?
Dear Gromacs Researchers, My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to extend it to 100 ns. As shown on http://www.gromacs.org/Documentation/How-tos/Extending_Simulations Should I use the following two lines of code for the files in the same folder? grompp -f new.mdp -c old.tpr -o new.tpr -t old.cpt gmx mdrun -deffnm new -cpi -append Thank you. Yours sincerely Cheng -- 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.
