[gmx-users] Lennard-Jones Parameters

Justin Lemkul jalemkul at vt.edu
Fri Oct 12 15:14:58 CEST 2012

On 10/12/12 8:04 AM, cuong nguyen wrote:
>   Dear Gromacs Users,
> I got the .gro and .top files of 1-octanol downloaded from PRODRG website.
> Please let me know if I can change charge, epsilon and sigma of the
> molecule as written in a paper? and How to do?

Atom types from PRODRG rarely, if ever, need changing.  Charges can be taken 
first by chemical homology (group-based approach that makes Gromos force fields 
convenient) and then by calculating the charges yourself.  For 1-octanol, it 
should be very straightforward to obtain parameters, zero charges on all the C 
atoms except for the one in the alocohol, then standard alcohol charges for the 
C-O-H.  Whether or not those parameters are sufficiently accurate is up to you 
to decide, but that's the approach one would take with this particular force field.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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