[gmx-users] pair types in FEP calculations

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 2 14:48:01 CEST 2011

Marcelino Arciniega Castro wrote:
> Hi there,
> Could someone please help to understand the use of function types 3 and 2 in the 
> [pairtypes ] directive in the topology file?
> I am trying to used it in a free energy calculation but the gromacs manual-4.5.4 in the
> page 112 is kind of confusing.

That information may be outdated.  The .mdp keyword "couple-intramol" seems to 
have the same function, negating the need to change anything in the [pairtypes]. 
  Just a guess.  Please test and see if your results are reasonable.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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