[gmx-users] Question about Thermodynamic Integration

Asaf Farhi asaf.farhi at weizmann.ac.il
Wed Aug 8 12:35:35 CEST 2012

Dear Justin

Thank you very much for the reply.
It's written in the manual:

5.7.4 Topologies for free energy calculations
Free energy differences between two systems, A and B, can be calculated as described in sec. 3.12.
Systems A and B are described by topologies consisting of the same number of molecules with
the same number of atoms.

Best regards,
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: Wednesday, August 08, 2012 1:05 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Question about Thermodynamic Integration

On 8/8/12 3:11 AM, Asaf Farhi wrote:
> Dear Gromacs users
> Hi. I wanted to ask about the use of Thermodynamic Integration.
> If the two compared molecules have a different number of atoms (e.g Theophylline and Methylxanithe) what should I do in order to simulate it well (it's written that you have to have the same number of atoms)?

If by "comparing molecules" you mean you are evaluating differences in, e.g.,
hydration free energy, there is no such requirement.  What I believe you are
thinking of is a FEP transformation between different species, an in silico
mutation process.  In that case, one would use dummy atoms that are transformed
into real interacting species over the course of the lambda-dependent
transformation.  In the case of TI, no such requirement exists.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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