I am getting the following warning message from g_rama, even for a simple system like a blocked Alanine dipeptide:
$ g_rama -s test.tpr -f traj.xtc […] Reading file test.tpr, VERSION 4.5.1 (single precision) Found 1 phi-psi combinations Dihedral around 6,8 not found in topology. Using mult=3 […] I have attached the files required to reproduce this problem. The two backbone dihedral angles for this systems are for the atom sets (5,7,9,15) and (7,9,15,17), and both groups appear in the [ dihedrals ] section of the topology file (and also exist in the tpr file). This happens using Gromacs 4.5.1 and 4.0.7. If you would like to reproduce this behavior, I have attached a small test set (never mind that the simulation doesn't necessarily make sense). I used the following sequence of commands: grompp -f test.mdp -c initial.gro -p topol.top -o test.tpr mdrun -s test.tpr g_rama -s test.tpr -f traj.xtc While the output of g_rama looks reasonable, the warning message makes me worried that I might have missed something in the topology file. Thanks, Lutz
test.mdp
Description: Binary data
initial.gro
Description: Binary data
topol.top
Description: Binary data
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