> > > Hi all, > I have to simulate peptide with SPC water model.During the simulation > trajectory peptide is some time going out of box through periodic > boundary condition is there but physical prescence of solvent is not > there, i mean if i have to extract water molecule within 3 angstrong > cutoff of peptide then it is not possible in all trajectory because of > some steps in which peptide is outside of box.I want to fix one of atom > in a box so that all in a process of folding simulation peptide will > remain inside of box. > I will be thankful for any positive response.
See http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions Mark _______________________________________________ gmx-users mailing list [email protected] http://www.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
