[gmx-users] Reducing Size of Data

[Justin A. Lemkul]

These step*.pdb are written when there is an instability in the system (i.e., on 
the verge of a crash).  You can usually map them to instances in the .log file 
of LINCS warnings or "water molecule could not be settled" reports.

-Justin

Jack Shultz wrote:
> Hi,
> 
> I am taking a look at reducing the size of my analysis. I've decreased
> log writing intervals. I notice mdruns generate these pdb files. Is
> there any way of reducing the frequency these files are written? I
> think that will go a long way to making my analysis easier.
> 
> 05/02/2009  07:34 PM           155,211 eiwit.pdb
> 05/02/2009  07:43 PM         8,251,350 step117b.pdb
> 05/02/2009  07:44 PM         8,251,361 step117c.pdb
> 05/02/2009  07:38 PM         8,251,350 step20b.pdb
> 05/02/2009  07:38 PM         8,251,361 step20c.pdb
> 05/02/2009  07:38 PM         8,251,350 step27b.pdb
> 05/02/2009  07:38 PM         8,251,361 step27c.pdb
> 05/02/2009  07:40 PM         8,251,350 step79b.pdb
> 05/02/2009  07:40 PM         8,251,361 step79c.pdb
> 05/02/2009  07:40 PM         8,251,350 step80b.pdb
> 05/02/2009  07:41 PM         8,251,361 step80c.pdb
> 05/02/2009  07:41 PM         8,251,350 step91b.pdb
> 05/02/2009  07:41 PM         8,251,361 step91c.pdb
> 05/02/2009  07:41 PM         8,251,350 step92b.pdb
> 05/02/2009  07:42 PM         8,251,361 step92c.pdb
> 05/02/2009  07:42 PM         8,251,350 step93b.pdb
> 05/02/2009  07:42 PM         8,251,361 step93c.pdb
> 05/02/2009  07:42 PM         8,251,350 step94b.pdb
> 05/02/2009  07:42 PM         8,251,361 step94c.pdb
> 05/02/2009  07:42 PM         8,251,350 step96b.pdb
> 05/02/2009  07:43 PM         8,251,361 step96c.pdb
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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