[gmx-users] Lennard-Jones Parameters
Peter C. Lai
pcl at uab.edu
Mon Oct 15 11:58:49 CEST 2012
On 2012-10-15 05:54:58AM -0400, Justin Lemkul wrote:
>
>
> On 10/15/12 5:45 AM, cuong nguyen wrote:
> > Dear,
> >
> > The top file downloaded from PRODRG did not consist of [atomtypes]. Please
> > tell me how can I add and use this function?
> >
>
> I see no need to change anything about the L-J parameters. Is there some reason
> you believe them to be incorrect? If you modify L-J parameters, you're no
> longer using Gromos96 43a1. In PRODRG topologies, the charges and charge groups
> certainly need changing, but I have never seen a need to hack the L-J parameters.
>
> -Justin
I think he needs to go back and ask the authors of the paper he is trying to
reproduce about how to parameterize 1-octanol according their specifications.
If they are using different LJ for the atoms in this molecule from 43a1 then
they are obviously not using gromos96 43a1 :)
>
> > Best regards,
> >
> > Cuong
> >
> > On 15 October 2012 16:43, Peter C. Lai <pcl at uab.edu> wrote:
> >
> >> 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 |
> >> ==================================================================
> >>
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>
> --
> ========================================
>
> 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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--
==================================================================
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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