AMBER Archive (2006)

Subject: Re: AMBER: Replica exchange

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Wed Jul 12 2006 - 09:25:14 CDT

I would suggest upgrading to Amber9, the REMD file handling
is much easier.

I do not see why it wants init.top.005- when I use amber8 it
never needs multiple prmtop files. maybe it would help if you
send your sander script so we can see your file assignments.

typically people want to analyze files at a single temperature,
sometimes you want to look at a single replica but more often the
ensemble at a single temperature is of interest. Which one you
use depends on what information you want to get from the
simulations.

Atsutoshi Okabe wrote:

>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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>>
>
>
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