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.
--Niel
________________________________________
From: Maryam Hamzehee [maryam_h_7860.yahoo.com]
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.
Cheers,
Maryam
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 22 2010 - 17:30:02 PST
