hamed amini wrote:
Dear Lemkul,
thank you very much for your quick respond.
But what parameters is involved in selection of force field? Is CHARMm27
selection good?
You should choose a force field based on whether or not it can accurately
describe the molecule(s) you're interested in simulating. You should spend
considerable time evaluating the literature to make an educated choice. No one
can supplant your judgment, and a careful choice made early will save you lots
of time (and wasted data) later.
-Justin
Best regards,
H. Amini
------------------------------------------------------------------------
*From:* Justin A. Lemkul <jalem...@vt.edu>
*To:* hamed amini <hamedamini...@yahoo.com>; Discussion list for GROMACS
users <gmx-users@gromacs.org>
*Sent:* Saturday, August 13, 2011 3:38 PM
*Subject:* Re: [gmx-users] aldehida
hamed amini wrote:
> Dear all,
>
> I want simulate a aldehida group near CNT. my aldehida has benzene as
functional group(-R). My first question is about suitable force field to
simulation of aldehida.What kind of force field you suggest? And also
Many could be used. Probably the only ones that can't immediately
handle it are the Gromos force fields.
> I know that one of the important force between CNT and
aldehida(benzene group) is pi-pi(in cnt and benzene). Do i need to
implement pi-pi interaction in the force field?
>
Such terms are not explicitly included in any of the force fields in
Gromacs.
-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
========================================
--
========================================
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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