I see. And how can I fix this ? Using trjconv -timestep ? I just want to be sure ...
Thank you On Fri, May 2, 2008 at 1:57 PM, Xavier Periole <[EMAIL PROTECTED]> wrote: > > You probably fond the problem. trjcat expects 10 ps intervals > between frames. If it is not the case it complains. > On Fri, 2 May 2008 13:14:07 +0200 > > "maria goranovic" <[EMAIL PROTECTED]> wrote: > > > I have gmxchecked my individual trr files. They should contain 10 frames > > each, but the output looks like: > > > > ##################### > > Reading frame 10 time 10002.000 > > Timesteps at t=10000 don't match (10, 2) > > Last frame 10 time 10002.000 > > > > > > Item #frames > > Step 11 > > Time 11 > > Lambda 11 > > Coords 11 > > Velocities 11 > > Forces 0 > > Box 11 > > > > gcq#54: "I'm a Wishbone and I'm Breaking" (Pixies) > > ##################### > > > > I think I have some idea of what the problem might be. I use the > > following > > method to continue my simulation trajectories: > > > > From the minimized structure, I first run a short 2 ps (1000 step) > > > > > simulation where I assign initial velocities. I obtain out-1.trr and > > out-1.edr and out-1.gro. I then want to use tpbconv to continue the > > simulation, like so: > > > > tpbconv -f out-1.trr -s out-1.tpr -e out-1.edr -extend 100 -o out-2.tpr > > > > However, out-1.tpr cannot be used to continue the simulation, because > > new > > velocities would be assigned, and I might want to change some parameter > > (like removing restraints) when I continue the simulation. So, I then > > make a > > new out-1.tpr file based on a dummy .mdp file, which contains all the > > new > > parameters for the continuation run, and which looks like: > > > > grompp -f dummy.mdp -c out-1.gro -p temp.top -o out-1.tpr > > > > ####### > > integrator = md > > tinit = 0 > > init_step = 1000 > > nsteps = 0 > > dt = 0.002 > > > > etc... > > ####### > > > > So, the new tpr file suggests that the simulation should start from > > 1000x > > 0.002 = 2 ps. This seems to be the source of the problem somehow, > > because > > the error when I use gmxcheck on the merger trajectory is typically > > like: > > > > Timesteps at t=21702 don't match (2, 8) > > > > So, there seems to be a 2 ps offset. the above output is also not very > > clear > > to me. What does (2,8) mean ? I hope this makes things a little more > > clearer. > > > > So there are no missing frames, but how do I fix the timestamps and so ? > > > > Thanks a lot for reading the long email and helping out > > > > -maria > > > > > > > > > > > > > > > > On Fri, May 2, 2008 at 12:25 PM, Xavier Periole <[EMAIL PROTECTED]> > > wrote: > > > > On Fri, 2 May 2008 12:01:37 +0200 > > > "maria goranovic" <[EMAIL PROTECTED]> wrote: > > > > > > > I used: > > > > > > > > trjcat -o out.trr -f *trr > > > > > > > It looks like you have missing frames in your xtc files ... that > > > happens sometimes when the simulation is stopped and restarted > > > from the trr file whereas the buffer of the xtc file is not emptied. > > > > > > Did you gmxcheck the xtc files? > > > > > > On Fri, May 2, 2008 at 11:42 AM, Mark Abraham < > > > [EMAIL PROTECTED]> > > > > wrote: > > > > > > > > maria goranovic wrote: > > > > > > > > > > > Hi, > > > > > > > > > > > > After using gmxcheck on a merged trajectory, I get the following > > > > > error > > > > > > throughout the trajectory. What does this mean ? > > > > > > > > > > > > > > > > How did you merge the trajectory? > > > > > > > > > > Thank you for the help. > > > > > > > > > > > > > > > > > > > > > > > > ..... > > > > > > Timesteps at t=21610 don't match (8, 10) > > > > > > Reading frame 50 time 21670.002 Timesteps at t=21700 don't > > > > > match > > > > > > (10, 2) > > > > > > > > > > > > Timesteps at t=21702 don't match (2, 8) > > > > > > > > > > > > Timesteps at t=21710 don't match (8, 10) > > > > > > Reading frame 60 time 21760.002 Timesteps at t=21800 don't > > > > > match > > > > > > (10, 2) > > > > > > .... > > > > > > > > > > > > and so on. > > > > > > > > > > > > > > > > > > -- > > > > > > Maria G. > > > > > > Technical University of Denmark > > > > > > Copenhagen > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > > > > > _______________________________________________ > > > > > > gmx-users mailing list [email protected] > > > > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > > > > Please search the archive at http://www.gromacs.org/searchbefore > > > > > > 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 mailing list [email protected] > > > > > 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 > > > > > > > > > > > > > > > > > > > > > > -- > > > > Maria G. > > > > Technical University of Denmark > > > > Copenhagen > > > > > > > > > > ----------------------------------------------------- > > > XAvier Periole - PhD > > > > > > NMR & Molecular Dynamics Group > > > University of Groningen > > > The Netherlands > > > http://md.chem.rug.nl/~periole <http://md.chem.rug.nl/%7Eperiole> < > > > http://md.chem.rug.nl/%7Eperiole> > > > > > > ----------------------------------------------------- > > > _______________________________________________ > > > gmx-users mailing list [email protected] > > > 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 > > > > > > > > > > > > -- > > Maria G. > > Technical University of Denmark > > Copenhagen > > > > ----------------------------------------------------- > XAvier Periole - PhD > > NMR & Molecular Dynamics Group > University of Groningen > The Netherlands > http://md.chem.rug.nl/~periole <http://md.chem.rug.nl/%7Eperiole> > ----------------------------------------------------- > _______________________________________________ > gmx-users mailing list [email protected] > 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 > -- Maria G. Technical University of Denmark Copenhagen
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