Thanks Mark. -- Sonali Dhindwal
--- On Fri, 13/8/10, Mark Abraham <mark.abra...@anu.edu.au> wrote: From: Mark Abraham <mark.abra...@anu.edu.au> Subject: Re: [gmx-users] Restarting the job To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Date: Friday, 13 August, 2010, 8:46 AM ----- Original Message ----- From: sonali dhindwal <sonali11dhind...@yahoo.co.in> Date: Friday, August 13, 2010 0:59 Subject: [gmx-users] Restarting the job To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Hello All, > > I have a query regarding the restarts of the jobs after crash. > I want to simulate a protein for 2 ns but in between due to system shutdown, > it stopped, and I made a restart using this command: > mdrun -s topol.tpr -cpi state.cpt -appendnow I checked the rmsd of in between > by producing a .xtc file of the job which ran till now and then checked g_rms > of the simulation, it is showing a graph like this,(I have attached in the > mail) See http://www.gromacs.org/Documentation/How-tos/Graphing_Data for a couple of gnuplot tips. I suspect the weirdness is gnuplot interpreting something as data that it should not interpret as data, and that the contents of the .xvg are actually the second half of normal RMS variation. > this is showing rmsd after the point the job was restarted with some error > in the beginning. > I want to know if there will be error at the end of the job too in the output > file, .gro ? The final .gro will have the final coordinates, as normal. Mark -----Inline Attachment Follows----- -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
