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
Received on Mon Jan 23 2012 - 01:30:03 PST
