[gmx-users] "alchemical" transformation

[Anton Feenstra]

Cristian Danciulescu wrote:
> 
> Dear gromacs users,
> Free energy differences between two systems A and B
> (aminoacids) can be calculated perturbing some parameters
> (masses, bonded and non-bonded interactions) in order to change
> the structure A to B.
> Some of the proper dihedrals that must be perturbed in the
> transformation A->B have different multiplicities. But multiplicities
> can not be perturbed during the free energy calculations.
> Could someone tell me how to solve or avoid this problem?

Define two dihedrals, one that will have parameters zero in the A
case, and the other zero in the B case.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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