AMBER Archive (2006)

Subject: AMBER: Replica exchange

From: Atsutoshi Okabe (okabe_at_cherry.bio.titech.ac.jp)
Date: Mon Jul 10 2006 - 06:38:17 CDT

Dear all,

 

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

 

sander -O -rem 1 -ng 16 -remlog rem.log -i REM.in -p INIT.top -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?

 

Atsutoshi

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