Hi, Luisa, I would first calculate the number of protons (H+) that you would find your water box. Then I would use the command genion to generate that number of H+'s that corresponds to the pH. Then I would use grompp to find out what the final charge is. If it is still negative, I would add NA+. If it is positive, I would add CL-. This should approximate the pH. Although there is one problem, ionizable residues. You will need to set those manually. I am not sure, if you can use the morse potential on specific residues instead of harmonic potential to make a residue ionizable. I hope this helps.
Best wishes, Art Roberts University of Washington Department of Medicinal Chemistry --- luisa pugliese <[EMAIL PROTECTED]> wrote: > Hello to everybody, > I am new to this mailing list and I am writing > because I wonder if anybody knows how can I set up > the pH of the system in gramacs. > Thank you to everybody > Luisa > ============================= > Luisa Pugliese, Ph.D. > [EMAIL PROTECTED] > S.A.F.AN. BIOINFORMATICS > Corso Tazzoli 215/13 -10137 Torino - ITALY > tel +39 011 3026230 > fax +39 011 3165080 > cell. +39 333 6130644 > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
