[gmx-users] periodic improper dihedral

[Eric Smoll]

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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