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<br><br>> From: giovanni.bussi@gmail.com<br>> Date: Mon, 14 Dec 2009 13:47:37 +0100<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] free energy perturbation<br>> <br>> Dear all,<br>> <br>> I am using GROMACS with free-energy perturbation to switch off a<br>> molecule gradually. If I understand correctly, the parameter<br>> "couple-moltype" is used to select which molecule to switch off. Is it<br>> possible to switch off *two* molecules at the same time? (e.g. a<br>> charged molecule and a neutralizing ion).<br><br>I have not implemented this yet.<br>It would indeed be useful.<br><br>> <br>> In case not, is there any problem related to the fact that in one of<br>> the topologies the total charge is not zero?<br><br>Yes, this will create problems, because you are then also calculating the cost<br>of building up a uniform backbground charge, both in case of PME and RF.<br><br>Note that free-energies of solvation of ions are huge numbers and are relatively<br>difficult to determine, both in simulation and in experiment.<br><br>There are two way to work around this problem:<br>Put both molecules together in one moleculetype definition.<br>Or simply manually set the LJ and charge of the ion to zero in the A or B state topology.<br><br>Berk<br><br>> <br>> Thanks a lot,<br>> <br>> Giovanni<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>                                            <br /><hr />New Windows 7: Simplify what you do everyday. <a href='http://windows.microsoft.com/shop' target='_new'>Find the right PC for you.</a></body>
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