[gmx-users] Lennard-Jones Parameters

Peter C. Lai pcl at uab.edu
Mon Oct 15 07:57:13 CEST 2012


It's hard to understand your question. What do you mean by "reference
parameters"? You said you already obtained a .gro and .top from PRODRG, which 
uses the gromos 43a1 forcefield to derive the parameters, so if you need
to change the LJ parameters, edit the top file it gave you.

If you want to reproduce the results of a published paper, you should use the 
forcefield and parameters specified in that paper and contact the author(s)
if more details are needed.

On 2012-10-15 10:42:57AM +0800, cuong nguyen wrote:
> 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?
> 
> Best regards,
> 
> Cuong
> 
> 
> 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
> >
> > --
> > ==============================**==========
> >
> > 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >
> > ==============================**==========
> > --
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Peter C. Lai			| University of Alabama-Birmingham
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