Jack,
Depending on how much free space you have, you may be able to run the
simulation until the end. You can convert it to gz after the fact. You
should calculate the total space it will take and see if you have enough
room.
If you don't, you will have to break your trajectory into pieces (stop now,
start a new one using binary). After they're all finished you can use ptraj
to put the pieces together.
I don't know if AMBER8 has binary output, I think it does but it's a
different format. You'll have to refer to the AMBER8 manual to see how to
use it.
Hope this helps!
-Dan
On Mon, Jan 23, 2012 at 6:10 PM, john Kerk <gor63.hotmail.de> wrote:
>
> Dear Dan
> thank you! my software is Amber8 and the total storage space of this
> partition is 120 GB. My simulation is running now, and approx. 700ps out
> of 2ns is comleted. Is this situation will lead to incomplete MD.crd file
> or can the program overwrite?
>
> Jack
>
>
> > From: sindhikara.gmail.com
> > Date: Mon, 23 Jan 2012 17:32:54 +0900
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] md.crd file is very large!
> >
> > A few points:
> >
> > 1) Nowadays it's highly recommended that you write your trajectories in
> > binary format (netcdf). Faster reading/writing, much less storage
> required.
> > >From the amber manual, SANDER input file section:
> > ioutfm Format of velocity and coordinate sets. As of Amber 9, the binary
> > format used in previous versions is no longer supported; binary output is
> > now in NetCDF trajec- tory format. Binary trajectory files are smaller,
> > higher precision and much faster to read and write than formatted
> > trajectories.
> > = 0 Formatted (default) = 1 Binary NetCDF trajectory
> >
> > 2) As for your trajectory you already ran, if you want to salvage it, you
> > can gzip it (I believe ptraj can read .gz format directly). If you are
> > desperate you might have
> > to strip the waters using ptraj.
> >
> > 3) If you have only a few 10s of GBs free on your disk, you may want to
> > look to upgrade. Either that or acknowledge that you're going to be
> limited
> > to relatively small systems.
> >
> > -Dan
> >
> > On Mon, Jan 23, 2012 at 5:22 PM, john Kerk <gor63.hotmail.de> wrote:
> >
> > >
> > > Dear Amber users
> > > I am ruuning a MD simulation experiment now to get (2ns trajectories)
> and
> > > my MD.crd file is very huge (i.e more than 11.6 GB). what should I do
> if
> > > there is no storage space on my hard disc. My OS is Ubuntu. What
> should I
> > > do?
> > >
> > > Jack
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Dr. Daniel J. Sindhikara
> > Institute for Molecular Science
> > E-mail: sindhikara.gmail.com
> > Website: http://sites.google.com/site/dansindhikara/
> > --
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
--
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 23 2012 - 01:30:03 PST
