[gmx-users] User-Specified LJ Epsilon and Sigma

[Phwey Gil]

Hi Justin, Maryam,

My initial problem was that I did not specify the atom types as Justin
said. Now I am able to change the masses and charges easily, but there are
still some problems with implementing the lennard-jones potential.

In my .itp file I write:
 [ atomtypes ]
     X  1  7.777  0.450  A  2  3

Where X is the atom in question, and I have made up numbers to see how they
appear in topol.tpr. I was able to see that the masses and charges can be
implemented straightforwardly. However, the C6 and C12 parameters are not
(2 and 3). The output values found in topol.tpr are:

 functype[9]=LJ_SR, c6= 1.41771114e+00, c12= 3.59777004e-01

Additionally, [ Bonds ] do not appear in the topol.tpr either.



On Wed, Sep 9, 2015 at 7:43 AM, Maryam Kowsar <maryam.kowsar at gmail.com>
wrote:

> Hi justin
> Actually i modified the forcefield parameters to introduce atoms that are
> not present in that. I think you are right in the case that we want to
> change bonded or nonbonded parameters in the forcefield
>
> On Wednesday, September 9, 2015, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 9/9/15 7:29 AM, Maryam Kowsar wrote:
> >
> >> Hi dan
> >> I think that's not possible to change forcefield parameters and use the
> >> old
> >> defined forcefield like opls. When you change the parameters in .itp you
> >> should introduce your own forcefield. Try to have all the needed files
> of
> >> forcefield in a new folder and use that during making topology.
> >>
> >>
> > This is not true. Any force field can be modified or extended. A local
> > copy of a modified force field is a safe recommendation, but in the case
> of
> > simply adding new atom types, there's little harm that can be done.
> >
> > -Justin
> >
> > On Tuesday, September 8, 2015, Phwey Gil <psg30 at case.edu> wrote:
> >>
> >> Hi,
> >>>
> >>> I am looking to specify my own parameters for LJ parameters. Using the
> >>> OPLS
> >>> forcefield, I only want to change the LJ parameters of some atoms.
> >>>
> >>> I have H2O, C8H16O2 (Octanoic acid) and C2H6O (Ethanol).
> >>> I am using SPC/E for H2O, and OPLS for C8H16O2 and C2H6O. And I want to
> >>> change the LJ parameters for the hydrogens in C8H16O2 only.
> >>>
> >>> I have tried specifying [ atomtypes ] in various places (In .top or
> .itp)
> >>> using the following format:
> >>>
> >>>   [ atomtypes ]
> >>>        H     H      1.008      0.450     A       5.66387665E-4
> >>> 2.80730518E-7
> >>>
> >>> But I was not successful; I checked topol.tpr and the numbers are
> >>> according
> >>> to OPLS and not my specified values.
> >>>
> >>> Can someone give me advice on how to do this? I've checked the forums
> >>> and I
> >>> was not successful at finding the correct information.
> >>>
> >>> Best Regards,
> >>>
> >>> Dan
> >>>
> >>> --
> >>> Dan Gil
> >>> Case Western Reserve University | Class of 2016
> >>> Researcher, Department of Chemical Engineering
> >>> psg30 at case.edu <javascript:;>
> >>> --
> >>> Gromacs Users mailing list
> >>>
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> >>>
> >>>
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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-- 
Dan Gil
Case Western Reserve University | Class of 2016
Researcher, Department of Chemical Engineering
psg30 at case.edu