[gmx-users] User-Specified LJ Epsilon and Sigma
Phwey Gil
psg30 at case.edu
Thu Sep 10 05:47:08 CEST 2015
Thank you for your help, Justin, Maryam, and Mark.
By following your advice, I was able to use my own LJ parameters for my
molecule. I used the following lines to be able to change atom X.
*In the topology.top:*
; Include forcefield parameters
#include "ffoplsaa.itp"
*#include "molecule.itp"*
*In molecule.itp:*
*[ atomtypes ]*
* ;name bondtype mass charge ptype sigma epsilon*
* X 1 18.998 -0.120 A 2.50000e-01
1.25520e-01*
[ moleculetype ]
PFOA 3
[ atoms ]
1 opls_961 1 PFOA CX3 1 0.360 12.011
2 opls_962 1 PFOA CX2 2 0.240 12.011
3 opls_962 1 PFOA CX2 3 0.240 12.011
4 opls_962 1 PFOA CX2 4 0.240 12.011
5 opls_962 1 PFOA CX2 5 0.240 12.011
6 opls_962 1 PFOA CX2 6 0.240 12.011
7 opls_962 1 PFOA CX2 7 0.240 12.011
8 opls_267 1 PFOA Coo 8 0.520 12.011
* 9 X 1 PFOA X 1*
* 10 X 1 PFOA X 1*
* 11 X 1 PFOA X 2*
* 12 X 1 PFOA X 2*
* 13 X 1 PFOA X 3*
* 14 X 1 PFOA X 3*
* 15 X 1 PFOA X 4*
* 16 X 1 PFOA X 4*
... *and so on...*
Sincerely,
Dan
On Wed, Sep 9, 2015 at 2:50 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> 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
> > > >>>
> > > >>> * Please search the archive at
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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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--
Dan Gil
Case Western Reserve University | Class of 2016
Researcher, Department of Chemical Engineering
psg30 at case.edu
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