AMBER Archive (2009)

Subject: Re: [AMBER] 60 giga output file .mdcrd file

From: Silvia Carlotto (silvia.carlotto_at_unipd.it)
Date: Tue Nov 03 2009 - 04:24:03 CST

Thanks to all,

I use the command Strip in ptraj and I obtaine a 5 Giga file. But now

the new problem is that vmd open only 2Giga file.

How can I split my mdcrd file in 3 smaller file?

I can't understand the command in amber tools

thanks to all

2009/11/3 Ross Walker <ross_at_rosswalker.co.uk>

> Hi Silvia,
>
> This sounds normal to me. Currently ptraj goes through and completely
> checks
> the mdcrd file before it processes it. If you figure that your system can
> do
> maybe 10MB per second sustained then just to run through a 60GB file
> without
> doing any processing will be 1.7 hours. Try just creating a copy of the
> file
> and this will give you an idea of the speed of your system, it will
> probably
> take > 30 mins just to copy. Then figure at least twice this for ptraj to
> process it for a basic strip command.
>
> Options are to 1) Get yourself a faster system, probably with multiple
> striped raid disks that will allow you to approach something like 120Meg a
> second.
>
> 2) rerun your simulation and do not save to the mdcrd file as often.
>
> 3) break up your mdcrd file into chunks or use ptraj to reduce the number
> of
> frames. This of course will still require you to run through it once.
>
> AmberTools 1.3 will be released soon and this includes several improvements
> for ptraj when working with large files, such as removing the initial check
> etc. It can also do parallel i/o so you can try to take advantage of
> parallel file systems such as GPFS or Lustre. In short though, if you are
> running this on your desktop, rather than a well build supercomputer
> connected by fiber to a true (and well designed) parallel file system then
> you are unfortunately up against the hardware limitations of your system.
>
> If you are using this on some NFS server that you are connecting to
> remotely
> then I would just take a weeks vacation while you wait for it to process.
>
> Sorry I can't help much more but unfortunately disk speeds have been
> largely
> flat for the last 8 years while capacity has ballooned.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> > Behalf Of Silvia Carlotto
> > Sent: Monday, November 02, 2009 9:42 AM
> > To: amber_at_ambermd.org
> > Subject: [AMBER] 60 giga output file .mdcrd file
> >
> > Dear user,
> >
> > I generate a.crd file of 60 Giga (a protein in a water box, 10 ns, n
> > tot
> > atom ca. 8000).
> >
> > I am using ptraj to strip water but
> >
> > the ptraj command is over 30 minutes on
> >
> > PTRAJ : trajin XXX.mdcrd
> >
> > checking coordinates : XXX.mdcrd
> > Is it a normal?
> >
> > Is it possible to manupulate with ptraj a file of these dimensions?
> >
> > I have no other ideas to strip water to generate a movie with vmd.
> >
> > thanks to help
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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> 

-- 
Silvia Carlotto, Ph.D

Università degli Studi di Padova
Dipartimento di Scienze Chimiche
via Marzolo 1, 35131 Padova

Telefono: +390498275124
E-mail: silvia.carlotto_at_unipd.it
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