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
--
========================================
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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