AMBER Archive (2006)

Subject: Re: AMBER: AMBER mdcrd file bigger than 2GB

From: Thomas Cheatham (
Date: Thu Jun 01 2006 - 11:25:19 CDT

> I do not want to lose my data. So, It is possible to split the amber mdcrd
> files in to small files. If yes then how?

(1) Process the file in ptraj to create two separate trajectories; this
requires two runs though the data. First, determine how many frames the
trajectory has...

rdparm prmtop
checkcoords mdcrd

This will report the number of frames in the trajectory file called
"mdcrd". For the sake of example, let's assume you have 500,000 frames.
Now you will want to run ptraj twice.

ptraj prmtop << EOF
trajin mdcrd 1 250000 1
trajout mdcrd_0-25k

ptraj prmtop << EOF
trajin mdcrd 2500001 9999999999 1
trajout mdcrd_25-50k

(2) Convert the trajectory to NetCDF or binpos; NetCDF requires AMBER9 and
support compiled into ptraj and will not produce a file that is much
smaller so I do not recommend this path forward. The binpos format will
be smaller, however it is not recognized by vmd.

(3) Create a smaller trajectory at a coarser resolution (i.e.
increase the spacing between frames...) Say we want every 5th frame
(offset = 5). If you do not know how many frames, choosing a very large
number will default the stop to the last frame.

ptraj prmtop << EOF
trajin mdcrd 5 999999999999 5
trajout mdcrd_by5

Good luck.

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