[gmx-users] Lennard-Jones Parameters

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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