[gmx-users] problem in ngmx
Ms. Aswathy S
aswathys at amritapuri.amrita.edu
Wed Jun 17 15:41:51 CEST 2009
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.
----- 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
> 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.
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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