[gmx-users] Lennard-Jones Parameters

cuong nguyen nvcuong68 at gmail.com
Mon Oct 15 09:53:54 CEST 2012


Thanks for you email.
I already had the .gro and .top files from PRODRG. Now I want to reproduce
these files following the LJ parameters in a published paper (charge, sigma
and epsilon values). I can change the charge in the top file, yet I do not
know how to change sigma and epsilon values.

Best regards,

Cuong

On 15 October 2012 13:57, Peter C. Lai <pcl at uab.edu> wrote:

> 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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