Hi ananya, You can get the coordinates using trjconv: trjconv -f <file.xtc> -s <file.tpr> -o <file.pdb> -b <initial time in ps> -e <final time in ps> this will give you pdb at the time you have mentioned.
For your first question- as far as I know you need to check whether there is any periodic image violation using g_mindist. Other things what you have to check depends on the parameter you want to see. Probably others may give a better answer regarding this. Bye kavya On Fri, Nov 9, 2012 at 5:04 PM, ananyachatterjee < ananyachatter...@iiserkol.ac.in> wrote: > > I am very new to this MD simulation, by reading the tutorials in the > website I have run an simulation and it is running from last 5 day and I am > not getting whether it is running properly or not. Could any one kindly > tell me how to see whether the simulation is running or not and also how > can I check the intermediate coordinated even when the simulation is > running. Kindly help me. > -- > Ananya Chatterjee, > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/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/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
