I will try the second solution you proposed (which seems more flexible). So, I should edit the top file (as explained in the "Topologies/File formats/Topologies for free energy calculations" section of the manual). And I should NOT use "couple-moltype" anymore, which is just a shortcut for the standard case of switching a single molecule. Right?
Thanks a lot Berk. Giovanni On Mon, Dec 14, 2009 at 3:49 PM, Berk Hess <[email protected]> wrote: > > >> From: [email protected] >> Date: Mon, 14 Dec 2009 13:47:37 +0100 >> To: [email protected] >> Subject: [gmx-users] free energy perturbation >> >> Dear all, >> >> I am using GROMACS with free-energy perturbation to switch off a >> molecule gradually. If I understand correctly, the parameter >> "couple-moltype" is used to select which molecule to switch off. Is it >> possible to switch off *two* molecules at the same time? (e.g. a >> charged molecule and a neutralizing ion). > > I have not implemented this yet. > It would indeed be useful. > >> >> In case not, is there any problem related to the fact that in one of >> the topologies the total charge is not zero? > > Yes, this will create problems, because you are then also calculating the > cost > of building up a uniform backbground charge, both in case of PME and RF. > > Note that free-energies of solvation of ions are huge numbers and are > relatively > difficult to determine, both in simulation and in experiment. > > There are two way to work around this problem: > Put both molecules together in one moleculetype definition. > Or simply manually set the LJ and charge of the ion to zero in the A or B > state topology. > > Berk > >> >> Thanks a lot, >> >> Giovanni >> -- >> 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 > > ________________________________ > New Windows 7: Simplify what you do everyday. Find the right PC for you. > -- > 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 > -- 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
