AMBER Archive (2006)

Subject: Re: AMBER: Replica exchange

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Mon Jul 10 2006 - 07:13:48 CDT

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 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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