Re: [AMBER] NetCDF AMBER file corrupted

From: Jason Swails <>
Date: Thu, 19 Mar 2015 11:26:55 -0400

On Thu, 2015-03-19 at 15:20 +0100, Jacopo Sgrignani wrote:
> Dear all
> I'm trying to analyse a file of a trajectory (90ns) for a quite big system
> (380000 atoms), however after 316 frames it starts to be corrupted and
> I'm unable to analyse it.

What do you mean "corrupted"? Some kinds of corruption (e.g., if one
frame is corrupted due to some kind of I/O issue) result in a trajectory
where you can just skip over a frame. Other kinds of corruption (like
when a file is truncated) have lost information in a way that cannot be

Exact input and output will give us a better idea of what is going on
than just calling it broken or corrupt.

There are some things you can look at yourself to figure some things
out. For instance, 380,000 atoms require 3x380,000=1.4M floating point
numbers for each frame. A 32-bit (4 byte) single precision float means
each frame should take *roughly* 4*1.4M/1024^2=4.34MB. If your file is
around 1.3 GB, then it only has about 316 frames worth of information at

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Mar 19 2015 - 08:30:02 PDT
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