[AMBER] calculation of rmsd with cpptraj

From: Krantzman, Kristin D <KrantzmanK.cofc.edu>
Date: Mon, 17 Aug 2015 19:53:05 +0000

Dear All,
I have a puzzle that I do not understand. I have a system with 5 molecules that have resid's 1, 2, 3, 4 and 5. When I select one residue and have cpptraj calculate the rmsd for a trajectory, the value is very small at all time steps, i.e. rms :1 out res1.rms. I get a small value for all time steps for all the residues, i.e. rms :2 out res2.rms, etc. However, if I calculate the rms for all of the residues (five total) collectively, i.e. rms :1-5 resall.rms, the value of rmsd is much larger and increases over time. Could anyone explain this discrepancy? I have this when I do the calculation on a wrapped trajectory and also when I include the keyword noimage. I have searched through the Amber archives and reference manual, and I cannot figure out what is incorrect.
Thank you.
Sincerely, Kristin

Kristin D. Krantzman
Professor, Department of Chemistry and Biochemistry
College of Charleston
Charleston, SC 29424
(843) 953-3378

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Received on Mon Aug 17 2015 - 13:00:03 PDT
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