Dear David, all, I'm not 100% sure that i'm doing everything right, mainly because I have found only a slight record about pairtypes 2,3 in the manual. And on the revision list for GROMACS 3.3 this feature is the very last on the list. So I wonder if it was really implemented in 3.3.1 release?
However, it seems to me that grompp (3.3.1) really disregards the interaction type for pairs. E.g. setting arbitary function type (like 8 or 9) for pair interactions gives no error message whereas doing the same for other forcefiels directives would yield an error: interaction type undefined. Thanks, Alexey > Alexey, > > > I notice you haven't received a response on this; if you are convinced > you're doing the right thing, you might try submitting a bugzilla so the > developers can reproduce your problem. > > Thanks, > David > > > > On 7/31/06, Alexey Shaytan <[EMAIL PROTECTED]> wrote: > >> 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 gmx-users@gromacs.org >> 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 >> >> > -- 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 gmx-users@gromacs.org 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
