AMBER Archive (2009)

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

From: Peter Schmidtke (
Date: Mon Nov 02 2009 - 12:40:48 CST

You maybe should split up your simulation in several smaller files. You can
then load them in ptraj by sequentially calling the trajin command.

60Gb is a lot and 30mn don't seem odd for this amount of data in the text

You could for instance load only 1000 snapshots (already a lot) in ptraj
(trajin yourfile.mdrc 1 1000)
strip waters and do a trajout to a mdrcd file (gzipped is better, or netcdf
even better).
Next turn you read 1001 to 2000 and so on.... a bit slow, but should be
possible to view pieces of the dynamics with vmd then...

Good luck


On Mon, 2 Nov 2009 18:41:32 +0100, Silvia Carlotto
<> wrote:
> 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


Peter Schmidtke

---------------------- PhD Student at the Molecular Modeling and Bioinformatics Group Dep. Physical Chemistry Faculty of Pharmacy University of Barcelona

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