Skip to content
GitLab
Closed
Issue created by Paul Bauer@acmnpvMaintainer

Grompp shows no warning when reading redundant dih. parameters for the same atomtype from different .itp files. - Redmine #2077

Archive from user: Elton Carvalho

If more than one file #included in the .top define parameters for the same type 9 dihedral, grompp throws no warning about overriding these parameters. Thus, the parameters effectively being used in the run are unclear to the user. grompp only throws warnings when the repeated dihedrals are on the same file.

As a minimal working example consists in #including in a .top twice the same file, which contains [ dihedraltypes ] directives with type 9 dihedrals in it.
Running grompp with a .top file constructed that way only throws warnings when the dihedrals are repeated in the same file.

The expected behavior (according to the documentation and the warning text) would be a warning that all dihedral definitions are being overriden when reading the second copy of the #include, since they are type 9 dihedrals involving the same 4 atomtypes in non-adjacent lines.

The attached tarball contains a charmm forcefield directory and a ddt.prm file defines a few dhedraltypes as type 9. The ddt.top file includes the ddt.prm file and then its identical copy ddt2.prm. Running grompp -f em.mdp -c cube.gro -p ddt.top throws two warnings. Commenting out the second and third multiplicities of the given dihedral eliminates the warnings.

(from redmine: issue id 2077, created on 2016-11-15 by gmxdefault, closed on 2017-02-06)

  • Changesets:
    • Revision 6b3b7474 by Berk Hess on 2017-01-20T14:46:15Z:
Disallow overwriting of dihedral type 9

It is no longer allowed to repeat blocks of parameter of multiple
lines for dihedrals of type 9. It is also no longer allowed to
override parameters or dihedrals of type 9. Both are too complex
to properly check. It is still allowed to repeat parameters blocks
consisting of a single line.
Repeating a block with the same parameters would lead to incorrect
dihedral potentials and forces.

Fixed bug in arrayref.h interfaces.

Fixes #2077.

Change-Id: I802c6714a9700744df4e6b5ea96e41aa82793388