AMBER Archive (2006)

Subject: RE: AMBER: Replica exchange

From: Atsutoshi Okabe (okabe_at_cherry.bio.titech.ac.jp)
Date: Tue Jul 11 2006 - 23:13:38 CDT

Dear Calros,

Thank you for your response.
I'm reading Amber8 manual on page 147 (Content of the ouput files)
carefully.
I think if I set repdrd=1, I can get mdcrd files containing data for a
particular
replica( continuous trajectory in phase space but discontinuous in target
temperature) So, can I choose any one of the mdcrd files at ramdom if I
will analize the trajectory sampling multiple temperatures?

> for the -rem 0 problem, you need to be more specific
> that just saying it failed. That doesn't give me enough information
> to help.
Actually I've got the following error message.

Unit 8 Error on OPEN: INIT.top.005

Why do I need INIT.top.00X files??

Also I've got 16 md.out files but nothing is written in these files. And I
couldn't get mdcrd files and mdrst files.

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Carlos Simmerling
Sent: Tuesday, July 11, 2006 9:49 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: Replica exchange

this is described on page 147 of the Amber8 manual.
the repcrd variable controls what is in your output files.

for the -rem 0 problem, you need to be more specific
that just saying it failed. That doesn't give me enough information
to help.

Atsutoshi Okabe wrote:

>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 md.in -p INIT.top -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
>calculation.
>
>Please give me any help!
>
>-----Original Message-----
>From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
>Carlos Simmerling
>Sent: Monday, July 10, 2006 9:14 PM
>To: amber_at_scripps.edu
>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 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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