[gmx-users] problem using pairtypes 2, 3 for free-energy decoupling

[David Mobley]

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 <shaytan at polly.phys.msu.ru> 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: shaytan at polly.phys.msu.ru
> Web: http://polly.phys.msu.ru/~shaytan/
>
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