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
input.
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:
http://www.gromacs.org/Documentation/How-tos/Parameterization
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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