Re: [AMBER] RMSD for two trajectories

From: Niel Henriksen <>
Date: Wed, 22 Dec 2010 18:20:30 -0700

You could combine the trajectories and use the "2drms" command.
You would have to be careful about prmtop compatibility though ...
It wouldn't be straightforward, but it might work.

From: Maryam Hamzehee []
Sent: Wednesday, December 22, 2010 5:31 AM
To: amber list
Subject: [AMBER] RMSD for two trajectories

Dear All

I have two trajectories of MD simulation related to wild type and mutant form of my ligand in the complex of receptor-ligand. I would like to compare the RMSD of pairwise structures but I have not found any option in VMD in order to do that. How can I compare the RMSD of two seperate trajectories.

Any help would be appreciated.


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Received on Wed Dec 22 2010 - 17:30:02 PST
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