[gmx-users] amber96 RB dihedrals in GMX 4.0 and 4.5

Badi' Abdul-Wahid cabdulwa at nd.edu
Mon Jan 24 18:53:40 CET 2011


I have prepared the same system (WW domain) with GMX 4.0.7 and
4.5.3 using amber96. Doing a gmxdump on the tpr files seems to
show that the RB dihedrals are absent from the 4.5-prepared
system, but present in the 4.0-prepared one. I used the same mdp
files for both GMX versions.

> gmxdump -s system.tpr | grep RBDI

Looking at the [dihedrals] directive in the topology file: 4.0
has funct 1 (proper dihedrals) and funct 3 (RB dihedrals) while
4.5 has funct 4 (improper) and funct 9 (proper) (pages 108 and
124 for the 4.0 and 4.5 respectively).

The 4.5 manual (page 129 under the [dihedrals] directive
description) seems to imply that the RB dihedrals need to be
added by hand and the 1-4 interaction in [pairs] should be
removed for the atoms involved in the RB dihedrals.
Is this correct?

What is the best way to prepare a system with Ryckaert-Bellemans dihedrals
in GMX 4.5?

Thanks for your time.


Badi' Abdul-Wahid
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