Re: [AMBER-Developers] netcdf restart files?

From: B. Lachele Foley <>
Date: Wed, 12 Jan 2011 04:32:58 +0000

We're a bit snowed in here in Athens. UGA is closing tomorrow for the third day running. We might not be so fast at testing, but I promise we'll do it soon. Thanks for doing that!

:-) Lachele

Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA

From: Daniel Roe []
Sent: Tuesday, January 11, 2011 10:59 PM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] netcdf restart files?

Hi all,

Sander can now read the netcdf restart format as well as write.
Reading the format is currently controlled through the use of ntx.
ntx=8 reads coordinates only (analogous to ntx=1), and ntx=9 reads
coordinates and velocities. As with standard restart files the box
information is read in the ewald setup routines; the netcdf restart
format is automatically detected there.

The netcdf restart format could also be automatically detected in the
getcor() routine, but I figured it's better (at least initially) to
keep file behavior consistent. It can be easily changed so that ntx is
for example automatically chosen (8 or 9) if a netcdf restart is
detected as INPCRD and based on the value of irest.

Please experiment if you want and let me know if there are any
problems with the format.


On Mon, Jan 10, 2011 at 1:06 PM, Daniel Roe <> wrote:
> Hi All,
> I have implemented some experimental code in sander and cpptraj for
> reading and writing restart files in a netcdf format. Right now the
> restart includes coordinates and velocities (double precision), time,
> title, and (if performing REMD) replica temperature; they don't yet
> include any other info such as the state of the RN generator etc,
> although this should not be hard to add.
> To use the netcdf restart format in sander set ntxo = 2. Currently
> sander will only write the format - I'm working on the reading part
> now. Cpptraj will both read and write the format.
> -Dan

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