[gmx-users] aldehida

[Justin A. Lemkul]

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 <jalemkul at vt.edu>
> *To:* hamed amini <hamedamini_84 at yahoo.com>; Discussion list for GROMACS 
> users <gmx-users at 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

========================================