Re: Is the DCD file size consistent for consecutive runs?

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Oct 08 2010 - 09:21:52 CDT

If that is the pattern then you should be able to reproduce the truncation
effect by repeating an earlier run. Have you tried this?

-Jim

On Fri, 8 Oct 2010, Bjoern Olausson wrote:

> On Thursday 07 October 2010 23:42:07 Jim Phillips wrote:
>> Hi,
>>
>> The truncated DCD files are strange, since the trajectory, restart, and
>> output writes are all called from the same function. I see that the close
>> call on the dcd file wasn't error-checked. I'm adding that now so it will
>> be in tonight's build to at least flag the errors.
>>
>> Do the log files for the broken trajectories include the line "CLOSING
>> COORDINATE DCD FILE" and are there "WRITING COORDINATES TO DCD FILE AT
>> STEP" lines where they should be?
>>
>> Thanks.
>>
>> -Jim
>
> I just noticed that the truncated dcd files occurred every 90 runs starting
> from 52+90=142 142+90=232 232+90=322 so the next might occur at 322+90=412
>
> I am currently at run343 ...
>
> Strange!
>
> I attached a link to my python script just in case but I doubt it has anything
> to do with the truncation.
> http://olausson.de/scriptarchive/16-modeling/78-runibverbs-npgtpy
> (Scroll to the bottom to download it as a file)
>
> Cheers
> Bjoern
>
> --
> Bjoern Olausson
> Martin-Luther-Universitšt Halle-Wittenberg
> Fachbereich Biochemie/Biotechnologie
> Kurt-Mothes-Str. 3
> 06120 Halle/Saale
>
> Phone: +49-345-55-24942
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:35 CST