[AMBER] Extracting replica trajectories

From: Cheng-I Lee <biocil.ccu.edu.tw>
Date: Sun, 20 Feb 2011 17:11:04 +0800

Dear Amber users,

I have followed the AMBER tutorial A7 for REMD simulation.
In analysis of the REMD results, reolica trajectories can be extracted by a
script named create_replica_trajs.x
In this script, what kind of distance information is obtained?

ptraj ala10.prmtop << EOF
trajin remd.mdcrd.$ext
trajout remd.reptraj.$ext nobox

distance d1 out dist.rep.$ext :2.CA :8.CA

Also, the manual of AMBER 11 does not include the section of ptraj. I
assumed that ptraj in AMBER 11 works as same as in AMBER 9.

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Received on Sun Feb 20 2011 - 01:30:03 PST
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