Dear Michael, Berk, all I'm currently trying to use GROMACS for calculation of solvation free energies for small molecules in water and hexane.
Searching through the mailing archives I found the following method to decouple solvent-solute interactions: Berk Hess Wed Mar 1 09:30:25 CET 2006 wrote: >The idea is that for the solute to be decoupled one would replace >the in its [ pairs ] section type 1 by type 2 >and exclude all intramolecular non-bonded interactions and replace >add them again explicitly in a [ pairs ] section as type 3. > However, trying to realize this method in GROMACS 3.3.1 release I encountered a problem: it seems that in my case grompp or mdrun disregards the type of pair interaction, assuming it always to be 1. And the pair interactions ARE pertubed during the free energy calculation. So setting the pairs topology parameters as -------------------- [ pairs ] ; ai aj funct 2 5 1 ........ -------------------- or ---------------------- [ pairs ] ; ai aj funct 2 5 2 .......... --------------------- yields the same results, when the free energy lambda is set to 1 (topology B). In my case the pair interactions are switched off, that is undesirable. Can anybody help me to figure out what the problem can be? Thanx in advance, Alexey -- Alexey Shaytan Chair of Polymer and Crystal Physics Faculty of Physics Moscow State Lomonosov University Tel: +79037411176 e-mail: [EMAIL PROTECTED] Web: http://polly.phys.msu.ru/~shaytan/ _______________________________________________ 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
