Hello
Context: 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? Question: 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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