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

[Mark Abraham]

Hi,

On Wed, Sep 9, 2015 at 7:55 PM Phwey Gil <psg30 at case.edu> wrote:

> 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
>

LJ parameters for the two atom types involved in an interaction combine
according to the equations in chapter 4 of the manual. There's been some
pre-computation already.

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

Well, don't ask grompp to convert your bonds into constraints ;-)

Mark


> 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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> > >>> posting!
> > >>>
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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
> --
> Gromacs Users mailing list
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