[gmx-users] problem in ngmx

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 17 15:05:01 CEST 2009

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.


> 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


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