[gmx-users] Free Energy Question

Emanuel Birru Emanuel.Birru at monash.edu
Tue Oct 4 01:49:30 CEST 2011

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.


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 

-----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
gmx-users mailing list    gmx-users at gromacs.org
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

More information about the gromacs.org_gmx-users mailing list