[gmx-users] Help with free energy

Justin A. Lemkul jalemkul at vt.edu
Sat May 5 04:59:01 CEST 2012

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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