AMBER Archive (2009)

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

From: Silvia Carlotto (silvia.carlotto_at_unipd.it)
Date: Mon Nov 02 2009 - 11:41:32 CST

 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
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