[gmx-users] multiple dihedrals of P-O bonds

Benno Portmann benno.portmann+gmx at ruhr-uni-bochum.de
Thu Jan 23 17:32:26 CET 2003


when creating a topology for ATP the dihedrals for -P-OM- or -OS-P-
dihedrals should be made by two cos(..) functions according the
forcefield definition in Gromos96 forcefield as well as in gromacs
forcefield. The
parameters in ffgmxbon.itp are

   OS    P    1     0.000       1.046      3
   OS    P    1     0.000       3.138      2

These both entrys should be added for each dihedral in the evaluation.

When creating a .tpr file using grompp the first of these two dihedrals
seems to be overwritten, gmxdump only gives the second dihedral. In
Gromacs Version 3.1.2. grompp overwrites the "multiple"-dihedals
noiseless, in Version 3.1.4. it gives warnings. The same happens with
dihedrals containing "CS"-atomtypes.

Any suggestions what to do?

-------------- next part --------------
A non-text attachment was scrubbed...
Name: benno.portmann+gmx.vcf
Type: text/x-vcard
Size: 344 bytes
Desc: Card for Benno Portmann
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20030123/22e2dcd8/attachment.vcf>

More information about the gromacs.org_gmx-users mailing list