[gmx-users] topology for free energy by perturbation

Alessandra Villa A.Villa at chem.rug.nl
Mon Aug 26 10:53:37 CEST 2002

Hi Mikko,

On Mon, 26 Aug 2002, Mikko Huhtala wrote:

> I'm not at all familiar with free energy perturbation
> calculations. I'd like to calculate the free energy difference between
> two small-molecule ligand complexes of a protein. The difference
> between the ligands is a replacement of one -OH group with
> -NH+(CH3)2. Is this too big a difference for perturbation? If not, how
> should the topology be constructed? Can dummy atoms be added to the
> -OH group and then be perturbed into -CH3s?

yes, only if the torsion multiplicity of -*-O- is the same of the torsion 
-*-N- . (see the manual)
If not , I suggest you to mutate  -O-H in dummy and  grow -NH+(CH3)2
group from dummy to real atom. 

best regards 

> Mikko
> _______________________________________________
> gmx-users mailing list
> gmx-users at 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 gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list