Dear Teobaldo, I think your calculation should be as easy as: " g_msd -n index.ndx " where index.ndx contains the atom numbers belonging to that "one molecule in water".
Good luck, Vitaly > Dear Users > I want to calculate the diffusion constant of one molecule in water.I make > this calculation in the followin way: > Obtaining a continuos trajectory > 1) trjconv -f traj.trr -pbc nojump -o traj_nojump.xtc > > Obtaining the msd of the solute, removing the center of mass of the system > Firt way: > 2a) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -o msd_solute.xvg > -rmcomm > I choose SOLUTE > > Second way > > 2b) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -rmcomm -o > msd_solute.xvg -rmcomm -mv > I choose SOLUTE > > There are significative differences in the results? > according to the gromacs manual -mv option is used in molecules, > > What is the correct step, 2a or 2b? > > > Regards > Teobaldo > -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
