[gmx-users] PBC problems??

Steve Seibold stevesei at ymail.com
Fri May 23 21:17:34 CEST 2014

My protein breaks according to viewing the traj in VMD and graphing the RMSD of the protein C-terminus 

I have tried all combinations of "trjconv -pbc -center
-box center" and nothing works..I was able to get online and find a
tutorial that says trjconv -pbc mol, should stop the problem, but this
failed....Isn't there a way for the protein and water to be wrapped or COM
calculations done DURING MD to remove translation, rotation so that post-MD
modification of trajectories is unnecessary??...If I make an index group of the
N-terminus of the protein this problems goes away or if I use the whole
protein...It is only when I attempt to get the rms of the C-terminus region
that I get this graphing problem (traj plots look like Histograms)....Not sure what this means since if I observe
the trajectories in VMD the whole protein breaks up....

Thanks, Steve

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