Re: AMBER: Replica exchange

From: Carlos Simmerling <carlos.csb.sunysb.edu>
Date: Mon, 10 Jul 2006 08:13:48 -0400

can you tell us which Amber version you are using?


Atsutoshi Okabe wrote:

> 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 Iíve 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 donít 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 Ö... So What the REM.trj file means ?
>
> Could you please give me any help?
>
> Atsutoshi
>
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Received on Wed Jul 12 2006 - 06:07:10 PDT
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