[gmx-users] Lennard-Jones Parameters

[Peter C. Lai]

Is there no [atomtypes] section in the top file?

On 2012-10-15 03:53:54PM +0800, cuong nguyen wrote:
> 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
> > Programmer/Analyst              | KAUL 752A
> > Genetics, Div. of Research      | 705 South 20th Street
> > pcl at uab.edu                     | Birmingham AL 35294-4461
> > (205) 690-0808                        |
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-- 
==================================================================
Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
(205) 690-0808			|
==================================================================