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

Alexey Shaytan shaytan at polly.phys.msu.ru
Mon Jul 31 17:18:44 CEST 2006

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
[ 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

Can anybody help me to figure out what the problem can be?

Thanx in advance,

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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