[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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