AMBER Archive (2006)

Subject: AMBER: Replica exchange

From: Atsutoshi Okabe (
Date: Mon Jul 10 2006 - 06:38:17 CDT

Dear all,


I executed the following sander command to perform replica exchage MD(16


sander -O -rem 1 -ng 16 -remlog rem.log -i -p -c md.rst -x
REM.trj -r REM.rst -o REM.out"


Then I've got one REM.trj file and 16 REM.trj.000 ~ REM.trj.015 files.


I want to analize the trajectory generated by MD. But I don't know which trj
files I shold use.

I think the REM.trj.000 trajectory corresponds to the coordinate of replica1
and the REM.trj.001

Corresponds to replica2 .... So What the REM.trj file means ?


Could you please give me any help?



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