[Bulk] [gmx-users] Archiving all the simulation data

[David van der Spoel]

Tsjerk Wassenaar wrote:
> Hi,
> 
> There may be some use for velocities. E.g. in velocity autocorrelation, 
> but in that case you only need short simulations. Other uses could be 
> imagined though, but I don't think your involved in these (there are no 
> tools yet in Gromacs at least) :) Still, one thing you should probably 
> do is get rid of all those solvent molecules you're not interested in (I 
> guess). If required, you can first select the subset of water molecules 
> that is close to the solute.

Indeed, it depends on your application. We have just submitted a paper 
where we had to determine temperatures of subsystems for which we did 
not know the composition in advance. This could also happen if you want 
to study e.g. the temperature distribution in a volume.

> 
> Cheers,
> 
> Tsjerk
> 
> On 5/17/06, *Yang Ye* <leafyoung81-group at yahoo.com 
> <mailto:leafyoung81-group at yahoo.com>> wrote:
> 
>     We recently go into some acquisition of cheap SATA-based online storage.
>     It is still preferable to have online storage rather than DVD or tape.
>     And price-wise, it is cheap now to have TB-level storage.
> 
>     Regards,
>     Yang Ye
> 
>     Dallas B. Warren wrote:
>      > Not exactly specific GROMACS question, but looking for some
>     insight for
>      > those who are sure to be encountering the same issues.
>      >
>      > How are people now handling archiving the huge data files that are
>      > produced when going to large simulation boxes for long periods of
>     time?
>      >
>      > Until recently it has been find for me to put them onto DVDs, or
>     may be
>      > two or three.  But as the sims get bigger, that is getting to be
>     a pain
>      > to do.
>      >
>      > What are the options available?  Is there actually anything out there
>      > that can archive things when you are looking at 20-50G of data files?
>      > Or is the best option to just archive onto hard drives now?
>      >
>      > Catch ya,
>      >
>      > Dr. Dallas Warren
>      > Lecturer
>      > Department of Pharmaceutical Biology and Pharmacology
>      > Victorian College of Pharmacy, Monash University
>      > 381 Royal Parade, Parkville VIC 3010
>      > dallas.warren at vcp.monash.edu.au
>     <mailto:dallas.warren at vcp.monash.edu.au>
>      > +61 3 9903 9524
>      > ---------------------------------
>      > When the only tool you own is a hammer, every problem begins to
>     resemble
>      > a nail.
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> 
> 
> 
> -- 
> 
> Tsjerk A. Wassenaar, M.Sc.
> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> Dept. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4
> 9747AG Groningen, The Netherlands
> +31 50 363 4336
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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