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
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--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
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Received on Mon Jan 23 2012 - 01:00:02 PST
