Hi Omer, My question was to how to avoid the "diffusion" of molecules out of the box during energy minimization and MD run? I think what you suggested here will just change the present trajectory into a new by using the pbc condition.
But i am wondering shouldnt this be done in MD calculation itself. It seems me to me that physics will be significantly different if i dont put the particles which go out of the box, back into the box. In that way the box will keep on expanding as i increase my simulation time and the calculated equilibirium properties wont be very meaningful and will fluctuate more than they really should. By the way i am talking about long chain lipid molecules here and i am using an all bond constraint. Amit On Tue, Sep 29, 2009 at 5:17 AM, Omer Markovitch <[email protected]> wrote: > Trj "trjconv -pbc nojump", or "trjconv -h" and read the short help printed. > Omer. > > >> >> I actually didnt realize this until i did a long simulation after which >> the trajectories of some of the atoms looked way out of the box dimensions. >> The co-ordinates of many atoms didnt lie in the box range. Although the >> output file contained the same box dimensions as I started with. Could >> someone help me in understanding what happened? >> >> > > _______________________________________________ > 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 >
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