Hi, visualize your MD trajectory in VMD without water (or solvent) and without ions (if have). I hope this helps.
Regards, Javier 2012/10/6 Albert <[email protected]> > hello: > > I am using the following command for md production in gromacs: > > grompp -f md.mdp -p md.top -o md.tpr > > mpirun -np 64 mdrun -s md.tpr -x md.xtc -g md.log > > However, I found that the md.xtc file need command: > > trjconv -f md.xtc -o convert.xtc -pbc mol > > to put the molecule in the centre of pbc box, otherwise it is messy when > we visualize in VMD. I am wondering, is it possible to ask mdrun generate > the .xtc file cetering the molecule in PBC box automatically and we no > longer need to use trjconv command to convert it. > > thank you very much > best > Albert > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
