[gmx-users] Free Energy Question

[Emanuel Birru]

I think using Perturbation method is more appropriate for this kind of free energy calculation. Check Leach, Molecular Modelling Principle and Applications pp 554-568. Its clearly described there and you can implement it in GROMACS.

Cheers,
Emanuel







=========================================================
Emanuel Birru
PhD Candidate

Faculty of Pharmacy and Pharmaceutical Sciences
Monash University (Parkville Campus)
381 Royal Parade, Parkville
Victoria 3052, Australia

Tel: Int + 61 3 9903 9187
E-mail: emanuel.birru at monash.edu 
www.pharm.monash.edu.au

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Fabian Casteblanco
Sent: Tuesday, 4 October 2011 6:28 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Free Energy Question

Hello all,

I have a general question about calculating free energies.  I recently
used g_bar to calculate the free energies of decoupling coulombic and
vdW forces of a solute molecule in solvent.  I now need to calculate
the free energy of a solute molecule mutating to a new molecule
(identical but with an extra -CH3 group) in a vacuum and in a solvent.
 Does anybody know if it would be better to use g_Bar again but this
time having the extra -CH3 group completely decoupled by itself or
with it be better to use the older slow-growth method that the Gromacs
Manual talks about in Sec 3.12.  I'm not sure if there is a way to
only decouple a certain part of a molecule using the g_bar method,
rather than decoupling the entire molecule.


Thanks for your help.

--
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.casteblanco at gmail.com
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