VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Jul 20 2012 - 01:40:50 CDT

You misunderstand how restartFreq works. There will never be more than two sets of restart files, one for the most recent output and one for the previous output.

-----Original Message-----
From: amin_at_imtech.res.in [mailto:amin_at_imtech.res.in]
Sent: Friday, July 20, 2012 1:41 AM
To: JC Gumbart
Subject: Re: vmd-l: Joining DCD files with overlapping frames.

Thanks. But my dcd frequency in 500 and a restart frequency of 500 will make a whole lot of files.So I have kept restart frequency to 50000. Do you suggest making restart frequency 500? even in that case can you please suggest a solution to my current problem?

Amin.

> If you set your dcdFreq to the same as your restartFreq, then there
> should be no overlap.
>
> On Jul 19, 2012, at 9:53 PM, amin_at_imtech.res.in wrote:
>
>> Dear all,
>> I have five dcd files from simulation runs started using restart
>> files of the previous run. Now, because I kept getting 'periodic cell
>> has become too small', so I restarted from the latest available
>> restart files. So, each of my dcd file has some frames common with
>> the previous one. I think I can chop the overlapping frames from the
>> each of the dcd files and then join them using catdcd, but is there a better way of doing this?
>>
>> Regards.
>> Amin.
>>
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>
>
>

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