Re: [gmx-users] changing the time step with tpbconv
OZGE ENGIN wrote: Thank you David, for your quick reply. However, I could not understand the reason why I have to turn on unconstrained_start option. That is if you want to do a continuation simulation. If the continuity is not an issue you can leave it off. -Original Message- From: David van der Spoel <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Date: Fri, 21 Mar 2008 17:03:06 +0100 Subject: Re: [gmx-users] changing the time step with tpbconv OZGE ENGIN wrote: Hi all, I am performing an 80-ns simulation. During the optimization of the parameters that were used in this run, I had performed some small test simulations, and used short frequency values to write the velocities. Unfortunately, I did not change this value into a bigger one before starting the main (longer) simulation. Consequently, I want to change the time step and use tpbconv to restart. Is there any way to do that? not with tpbconv, but with grompp -t -e -s -o you can do the same (with a new mdp file where you have to turn on unconstrained_start and to turn off gen_vel). Thanks in advance... Ozge Engin = Computational Science & Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] changing the time step with tpbconv
Thank you David, for your quick reply. However, I could not understand the reason why I have to turn on unconstrained_start option. -Original Message- From: David van der Spoel <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Date: Fri, 21 Mar 2008 17:03:06 +0100 Subject: Re: [gmx-users] changing the time step with tpbconv OZGE ENGIN wrote: > Hi all, > > I am performing an 80-ns simulation. During the optimization of the > parameters that were used in this run, I had performed some small test > simulations, and used short frequency values to write the velocities. > Unfortunately, I did not change this value into a bigger one before starting > the main (longer) simulation. Consequently, I want to change the time step > and use tpbconv to restart. > > Is there any way to do that? not with tpbconv, but with grompp -t -e -s -o you can do the same (with a new mdp file where you have to turn on unconstrained_start and to turn off gen_vel). > > Thanks in advance... > Ozge Engin > = > Computational Science & Engineering > Koc University > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Ozge Engin = Computational Science & Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] changing the time step with tpbconv
OZGE ENGIN wrote: Hi all, I am performing an 80-ns simulation. During the optimization of the parameters that were used in this run, I had performed some small test simulations, and used short frequency values to write the velocities. Unfortunately, I did not change this value into a bigger one before starting the main (longer) simulation. Consequently, I want to change the time step and use tpbconv to restart. Is there any way to do that? not with tpbconv, but with grompp -t -e -s -o you can do the same (with a new mdp file where you have to turn on unconstrained_start and to turn off gen_vel). Thanks in advance... Ozge Engin = Computational Science & Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] changing the time step with tpbconv
Hi all, I am performing an 80-ns simulation. During the optimization of the parameters that were used in this run, I had performed some small test simulations, and used short frequency values to write the velocities. Unfortunately, I did not change this value into a bigger one before starting the main (longer) simulation. Consequently, I want to change the time step and use tpbconv to restart. Is there any way to do that? Thanks in advance... Ozge Engin = Computational Science & Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
