[gmx-users] periodic improper dihedral

[Mark Abraham]

Hi,

Seeing the actual contents (e.g. via file sharing service) and error
message is usually better for finding the problem.

Mark

On Thu, 17 Dec 2015 12:29 Eric Smoll <ericsmoll at gmail.com> wrote:

> Hello Mark,
>
> Thanks for the response. I am having trouble finding this "mismatch" and I
> want to make sure the overall procedure is correct. I outline a schematic
> below:
>
> ******************** I add to the atomtypes file.
> opls_1000 12.011
> opls_1001 12.011
> etc...
>
> ******************** In the oplsaa.ff directory, I add:
>
> [ atomtypes ]
> opls_1000  A_B  12  12.011  0.0  A  1.0e-01  1.0e-01
> opls_1001  C_D  12  12.011  0.0  A  1.0e-01  1.0e-01
> opls_1002  E_F  12  12.011  0.0  A  1.0e-01  1.0e-01
> opls_1003  G_H  12  12.011  0.0  A  1.0e-01  1.0e-01
> etc...
>
> [ bondtypes ]
> A_B  C_D  1  1.0  1.0
> etc...
>
> [ angletypes ]
> A_B  C_D  E_F  1  1.0  1.0
> etc...
>
> [ dihedraltypes ]
> A_B  C_D  E_F  G_H  5  1.0  1.0
> etc...
>
> [ dihedraltypes ]
> A_B  C_D  E_F  G_H  4  1.0  1.0
> etc...
>
> ******************** Our CWD .itp files contain the following:
>
> [ moleculetype ]
> ; Name nrexcl
> TMP 3
>
> [ atoms ]
> ;     nr    type  resn  residue     atom  cgnr  charge      mass  typeB
> chargeB     massB
> 1  opls_1001  1  TMP  C1  1  0.0 12.011
> 2  opls_1002  1  TMP  C2  2  0.0 12.011
> 3  opls_1003  1  TMP  C3  3  0.0 12.011
> 4  opls_1004  1  TMP  C4  4  0.0 12.011
> etc...
>
> [ bonds ]
> 1  2  1
> etc...
>
> [ angles ]
> 1  2  3  1
> etc...
>
> [ dihedrals ]
> 1  2  3  4  5
> etc...
>
> [ dihedrals ]
> 1  2  3  4  4
> etc...
>
> ******************** The .top just includes the .itp's
>
> #include "oplsaa.ff/forcefield.itp"
> #include "TMP.itp"
>
> [ system ]
> TMP
>
> [ molecules ]
> TMP 1000
>
> ****************** Following this procedure, grompp delivers the error:
>
> ERROR 1 [file TMP.itp, line XXX]:
>   No default Improper Dih. types
>
> Is this workflow incorrect?
>
> Best,
> Eric
>
>
> On Wed, Dec 16, 2015 at 5:46 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > 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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