Re: [gmx-users] restart md from the point it had stopped
[Tsjerk] why do you write velocities and forces every 10 ps? Third world country my friend, energy supply is not that stable over here. Also the queue to run a process is huuuge, so every hour is important. In the end I do a trjconv to reduce # of frames. Great "Doing Restarts" whoever wrote it :D http://wiki.gromacs.org/index.php/Doing_Restarts On 10/9/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > sarbani chattopadhyay wrote: > > > > hi, > > I have been running a molecular dynamics simulation for 2 > > nanoseconds.But it stopped in > > the middle because of an internal problem.Is there any way to restart > > the simulation from > > the point it has stopped? > > See http://wiki.gromacs.org/index.php/Doing_Restarts for an expanded > discussion. > > Mark > ___ > 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 > -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. ___ 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] restart md from the point it had stopped
sarbani chattopadhyay wrote: hi, I have been running a molecular dynamics simulation for 2 nanoseconds.But it stopped in the middle because of an internal problem.Is there any way to restart the simulation from the point it has stopped? See http://wiki.gromacs.org/index.php/Doing_Restarts for an expanded discussion. Mark ___ 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] restart md from the point it had stopped
Hi Diego, gmxcheck will tell you whether the last frame is corrupted (incomplete) or not. Besides, why do you write velocities and forces every 10 ps? Do you have to much space on your hard-disk or do you need the velocities? Usually, writing to the .trr will be a compromise between the amount of disk space you have and the time you'll loose when restarting. I usually write one or two frames to the .trr per day. Cheers, Tsjerk On 10/8/07, Diego Enry <[EMAIL PROTECTED]> wrote: > > gmxcheck -f broken.trr > > check this information: > > Item#frames Timestep (ps) > Step 10110 > Time 10110 > Lambda10110 > Coords 10110 > Velocities 101 10 > Forces 101 10 > Box10110 > > I writing it every 1ps. > I recommend you NOT to use the LAST frame because it may be corrupted > if your simulation was terminated while writing this frame. To > continue, specify the frame just before the last one find above. > > tpbconv -s broken.tpr -f broken.trr -e broken.edr -o continue.tpr -time 9 > > Check If you write velocities&force to the .trr file, I think you > can't get a good continuation without that information. > > > On 10/8/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: > > Hi Sarbani, > > > > Use tpbconv. You can only (properly) restart from a point where you have > a > > frame with velocities (in the .trr file) and preferrably energies > (.edr). > > > > Best, > > > > Tsjerk > > > > > > On 8 Oct 2007 12:34:23 -, sarbani chattopadhyay > > <[EMAIL PROTECTED]> wrote: > > > > > > > > > > > > > > > hi, > > > I have been running a molecular dynamics simulation for 2 > > nanoseconds.But it stopped in > > > the middle because of an internal problem.Is there any way to restart > the > > simulation from > > > the point it has stopped? > > > > >Thank all > > > > > Sarbani > > > > > > > > > ___ > > > 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 > > > > > > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > Junior UD (post-doc) > > Biomolecular NMR, Bijvoet Center > > Utrecht University > > Padualaan 8 > > 3584 CH Utrecht > > The Netherlands > > P: +31-30-2539931 > > F: +31-30-2537623 > > ___ > > 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 > > > > > -- > Diego Enry B. Gomes > Laboratório de Modelagem e Dinamica Molecular > Universidade Federal do Rio de Janeiro - Brasil. > ___ > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] restart md from the point it had stopped
gmxcheck -f broken.trr check this information: Item#frames Timestep (ps) Step 10110 Time 10110 Lambda10110 Coords 10110 Velocities 101 10 Forces 101 10 Box10110 I writing it every 1ps. I recommend you NOT to use the LAST frame because it may be corrupted if your simulation was terminated while writing this frame. To continue, specify the frame just before the last one find above. tpbconv -s broken.tpr -f broken.trr -e broken.edr -o continue.tpr -time 9 Check If you write velocities&force to the .trr file, I think you can't get a good continuation without that information. On 10/8/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: > Hi Sarbani, > > Use tpbconv. You can only (properly) restart from a point where you have a > frame with velocities (in the .trr file) and preferrably energies (.edr). > > Best, > > Tsjerk > > > On 8 Oct 2007 12:34:23 -, sarbani chattopadhyay > <[EMAIL PROTECTED]> wrote: > > > > > > > > > > hi, > > I have been running a molecular dynamics simulation for 2 > nanoseconds.But it stopped in > > the middle because of an internal problem.Is there any way to restart the > simulation from > > the point it has stopped? > > >Thank all > > > Sarbani > > > > > > ___ > > 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 > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > ___ > 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 > -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. ___ 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] restart md from the point it had stopped
Please check the FAQ & list achives b4 posting. Your answer is already there. Is there any smart way to continue a run that crashed? http://www.gromacs.org/content/view/62/29/ -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. ___ 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] restart md from the point it had stopped
Hi Sarbani, Use tpbconv. You can only (properly) restart from a point where you have a frame with velocities (in the .trr file) and preferrably energies (.edr). Best, Tsjerk On 8 Oct 2007 12:34:23 -, sarbani chattopadhyay < [EMAIL PROTECTED]> wrote: > > > hi, > I have been running a molecular dynamics simulation for 2 > nanoseconds.But it stopped in > the middle because of an internal problem.Is there any way to restart the > simulation from > the point it has stopped? > > Thank all > > Sarbani > > > > ___ > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] restart md from the point it had stopped
hi, I have been running a molecular dynamics simulation for 2 nanoseconds.But it stopped in the middle because of an internal problem.Is there any way to restart the simulation from the point it has stopped? Thank all Sarbani___ 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
