Re: [AMBER] REMD production run restart

From: Sangita Kachhap <>
Date: Fri, 4 Feb 2011 23:11:13 +0530 (IST)

Thanks to reply
I have restarted REMD according to you and its running

> Hi,
> The '-A' flag tells sander to append to all output files (mdout, mdcrd
> etc) which can be a bit messy if all of your file names don't match up
> (plus there is potential to overwrite your input coordinates if e.g.
> you accidentally give them the same name as your restart files) so I
> personally wouldn't recommend it.
> In my opinion your best option is to restart the run in a separate
> directory using the restart files generated from the first run (i.e.
> the files specified by the '-r' flag in your groupfile). So for
> example, say your groupfile from the first run looks something like
> this:
> -O -rem 1 -remlog rem.log -i in.000 -p topology.parm7 -c
> initial.000.rst7 -o rem.out.000 -r run0.000.rst7 -x
> -O -rem 1 -remlog rem.log -i in.001 -p topology.parm7 -c
> initial.001.rst7 -o rem.out.001 -r run0.001.rst7 -x
> Copy the restart files (in this case run0.*.rst7) to a new directory.
> The groupfile for the restart run will look something like:
> -O -rem 1 -remlog rem.log -i in.000 -p topology.parm7 -c run0.000.rst7
> -o rem.out.000 -r run1.000.rst7 -x
> -O -rem 1 -remlog rem.log -i in.001 -p topology.parm7 -c run0.001.rst7
> -o rem.out.001 -r run1.001.rst7 -x
> Make sure that you have ntx=5 and irest=1 set in the input file of the
> restart run.
> -Dan
> On Fri, Feb 4, 2011 at 10:21 AM, Sangita Kachhap <> wrote:
>> Hello all
>> I am running REMD (production run) it has stooped running due to cluster
>> error.
>> I want to restart it.
>> As Amber manual there is option if use -A in command line it wiil help in
>> restarting
>> REMD simulation. I go through the amber mailing list there also I didnt get
>> any
>> idea.
>> can anyone sugesst to how restart REMD?
>> With regard
>> Sangita Kachhap
>> JRF
>> __________

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Received on Fri Feb 04 2011 - 10:00:04 PST
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