AMBER Archive (2009)

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

From: Richard Owczarzy (rowczarzy_at_idtdna.com)
Date: Tue Nov 03 2009 - 09:14:44 CST

Is it a limit of Windows and memory available to application? You do not have to load every frame to VMD. When you load the file, specify stride of 3. It is at the left buttom of the File Box. The VMD will load every 3rd frame of the trajectory, so 5/3 = 1.7 GB and you should be able to open the file.

Richard

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf Of Silvia Carlotto
Sent: Tuesday, November 03, 2009 4:24 AM
To: AMBER Mailing List
Subject: Re: [AMBER] 60 giga output file .mdcrd file

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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
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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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