[gmx-users] Lennard-Jones Parameters
nvcuong68 at gmail.com
Mon Oct 15 04:42:57 CEST 2012
Thank you very much for your email, Justin.
in case I want to use the reference parameters, which force-field and what
should I do to get the .gro and .top files for this molecule?
On 12 October 2012 21:14, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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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