AMBER Archive (2006)

Subject: RE: AMBER: Replica exchange

From: Atsutoshi Okabe (
Date: Mon Jul 10 2006 - 21:43:17 CDT

Dear Carlos,

I'm using Amber8.

I also want to perform no replica exchange for the initial 100ps before
exchange. So I set -rem 0 in sander command,

sander -O -rem 0 -ng 16 -remlog rem.log -i -p -c min.rst -x
md.trj -r md.rst -o md.out"

But the calculation was failed. I don't understand why I failed the

Please give me any help!

-----Original Message-----
From: [] On Behalf Of
Carlos Simmerling
Sent: Monday, July 10, 2006 9:14 PM
Subject: Re: AMBER: Replica exchange

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 -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?
> Atsutoshi

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