[gmx-users] Help with free energy

Emanuel Birru Emanuel.Birru at monash.edu
Sat May 5 09:06:39 CEST 2012

Hi Milinda,

There are different methods to do Free energy. I am using Thermodynamics Integration method; hence if you are interested to use TI I am willing to guide you, but I never use bar method. I did some parametrization so if you float your topology and mpd files I will give you some idea how to do it.


From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
Sent: Saturday, May 05, 2012 12:59 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Help with free energy

Please keep all correspondence on the gmx-users list.  I am not a private tutor
and you have better odds of solving your problem by allowing others to provide

On 5/4/12 8:01 PM, Milinda Samaraweera wrote:
> Hi Justin
> Im a very new to using Gromacs. I tried to reproduce the values in shirts paper
> for methane. And using a similar model for study the hydration of Anilinium. If
> I send you my input files could you please take a look and give me some suggestions.

Were you able to reproduce the methane hydration value?

Aniline and anilinium are different, with the latter being more difficult to
deal with on account of its charge.  If you post your topology, perhaps someone
will have some tips on how to modify it to produce better results, but proper
small molecule parameterization is not a task well-suited for new users.  It may
take considerable time and effort to derive a high-quality topology.  For
general advice, consult:




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

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