[gmx-users] periodic improper dihedral

[Mark Abraham]

Hi,

All that depends on is the atom types, so something there must not be
matching properly.

Mark

On Thu, 17 Dec 2015 10:15 Eric Smoll <ericsmoll at gmail.com> wrote:

> Thank you Mark,
>
> We are having difficulty adding new parameters to the oplsaa forcefield in
> "share/gromacs.top." We have a "[ dihedraltypes ]" directive where I add
> fourier dihedral parameters (function type 5) and a "[ dihedraltypes ]"
> directive where I add periodic improper dihedrals (function type 4). We
> have itp/top files that contain two corresponding "[ dihedrals ]"
> directive.
>
> Grompp is complaining that "No default proper/improper dihedral type."
> Grompp also complains when the improper terms are represented with a proper
> dihedral (function type 2).
>
> Do you have any idea how I could trouble shoot this problem?
>
> Best,
> Eric
>
> On Wed, Dec 16, 2015 at 4:54 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Yes
> >
> > On Thu, 17 Dec 2015 05:39 Eric Smoll <ericsmoll at gmail.com> wrote:
> >
> > > Hello GROMACS users,
> > >
> > > I have a question about specifying periodic improper dihedrals in
> > GROMACS.
> > >
> > > In the GROMACS manual (chapter 5, table 5.5), the parameters of the
> > > periodic improper dihedral are listed as follows:
> > >
> > > phi_s ( deg ); k_phi (kJ mol^-1); multiplicity
> > >
> > > In the GROMACS manual (chapter 4, equation 4.60), the form of the
> > periodic
> > > improper dihedral is specified as
> > >
> > > V_d( phi_ijkl ) = k_phi ( 1 - cos(n*phi - phi_s))
> > >
> > > Am I correct in assuming that "n" shown is the "multiplicity" listed
> > above?
> > >
> > > Best,
> > > Eric
> > > --
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