[gmx-users] problem in ngmx

[Ms. Aswathy S]

Ok. You meant I have to cross check these parameters before getting in to simulation.I will do that 

Thank you very much for your replies.

Dept. Biotechnology
Ext. 3108

----- Original Message -----
From: "Justin A. Lemkul" <jalemkul at vt.edu>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Wednesday, June 17, 2009 6:35:01 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: Re: [gmx-users] problem in ngmx



Marc F. Lensink wrote:
> On Wed, Jun 17, 2009 at 06:57:24AM -0400, Justin A. Lemkul wrote:
>> The .mdp file seems reasonable.  QM charges are not necessarily the end 
>> result in Gromos parameterization.  In fact, such calculations are often 
>> unnecessary. In my experience, assigning charges based on functional groups 
>> already present in the force field is often a reasonable starting point.  
>> But in any case, you must always verify your results and, in the end, 
>> follow the same parameterization scheme as the original force field (which, 
>> in the case of the Gromos force fields, does not include QM charge 
>> calculations).
> 
> I've run hundreds of QM charge calculations.  in many cases, they are
> remarkably similar to the gromos charges...
> 

Agreed.  The point I was trying to make (perhaps poorly) was that simply running 
a QM charge calculation and calling it done is not the right track.  I got the 
impression from the original post that charges were assigned and a simulation 
conducted without any validation of those parameters.

-Justin

> cheers,
> marc
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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