From: Felipe Merino (felipe.merino_at_mpi-dortmund.mpg.de)
Date: Wed Jul 22 2015 - 03:07:32 CDT
Hi,
That depends on whether you consider the intramolecular interactions or
not (alchDecouple on or off). Check the FEP tutorial.
Felipe
On 22/07/15 09:25, Mohan maruthi sena wrote:
> Dear all,
> I want to calculate free energy of solvation for a
> ligand in water using FEP method in NAMD. I read the following post in
> mailing list,
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2003-2004/0186.html,
> in which free energy solvation of methyl alchol is calculated as shown
> below,
>
> Asolv(MeOH) = A*(MeOH, vacuum) - A*(MeOH, water)
>
> where Asolv solvation free energy
> A* be the free energy of anihilation.
>
> My question is as follows,
> Is it not enough if we calculate
> the MeoH+water ------ dummy+water.
> Doesn't this corresponds to free energy of solvation of MeOH?
>
>
> Thanks & Regards,
> Mohan
-- Felipe Merino Max Planck Institute for Molecular Physiology Department of Structural Biochemistry Otto-Hahn-Str. 11 44227 Dortmund Phone: +49 231 133 2306
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