<div>Hello</div><div><br></div><div><br></div><div>Context:</div><div>I have prepared the same system (WW domain) with GMX 4.0.7 and</div><div>4.5.3 using amber96. Doing a gmxdump on the tpr files seems to</div><div>show that the RB dihedrals are absent from the 4.5-prepared</div>
<div>system, but present in the 4.0-prepared one. I used the same mdp</div><div>files for both GMX versions.</div><div><br></div><div>> gmxdump -s system.tpr | grep RBDI</div><div><br></div><div>Looking at the [dihedrals] directive in the topology file: 4.0</div>
<div>has funct 1 (proper dihedrals) and funct 3 (RB dihedrals) while</div><div>4.5 has funct 4 (improper) and funct 9 (proper) (pages 108 and</div><div>124 for the 4.0 and 4.5 respectively).</div><div><br></div><div>The 4.5 manual (page 129 under the [dihedrals] directive</div>
<div>description) seems to imply that the RB dihedrals need to be</div><div>added by hand and the 1-4 interaction in [pairs] should be</div><div>removed for the atoms involved in the RB dihedrals.</div><div>Is this correct?</div>
<div><br></div><div><br></div><div>Question:</div><div>What is the best way to prepare a system with Ryckaert-Bellemans dihedrals in GMX 4.5?</div><div><br></div><div><br></div><div><br></div><div>Thanks for your time.</div>
<div><br></div><div>--</div><div><br></div><div>Badi' Abdul-Wahid</div><div><br></div>