AMBER Archive (2009)

Subject: Re: [AMBER] bintraj and amber 10

From: Naser Alijabbari (na3m_at_virginia.edu)
Date: Wed Apr 22 2009 - 20:05:21 CDT

Is there any way to see the precision of what is written in the netcdf file?
For example when I convert from netcdf to ASCII format the resulting file
has the same number of digits (6 counting the decimal point). But what is
actually written into the netcdf file? is it 8 digit?

On Wed, Apr 22, 2009 at 6:59 AM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> Dear Naser
>
> > I am try the following command in Amber 10: ./configure_amber -bintraj
> > -openmpi ifort
> >
> > unknown flag -bintraj
>
> There is no -bintraj flag for AMBER 10 configure_amber anymore. Unlike
> Amber9 bintraj support is now the default so you just have the option to
> turn it off using the flag '-nobintraj'.
>
> Note, this is different to PMEMD compilation where you have to explicitly
> request bintraj support by specifying -bintraj.
>
> > ./configre_amber -help are "-nobintraj" (so I just tried IOUTFM=1 and
> > there
> > was no error but ptraj does not recognize the format so there is a
> > problem).
>
> Did you build ptraj (as part of amber tools ./configure_at) with netcdf
> support? This should be the default but there may have been problems during
> the build process or you are using an old version of ptraj without
> realizing
> it. Also make sure you have applied bugfix.3 for your AmberTools
> installation:
>
> http://ambermd.org/bugfixesat.html
>
> Programs: ptraj
>
> Description: Fixes multiple problems.
> 1) Ptraj did not correctly open netcdf files.
> 2) Ptraj misidentified Amber REMD restarts as trajectories.
> 3) io.c contained duplicate code in openFile() that resulted
> in strange behavior for bzipped files.
> 4) gzipped amber remd trajectories are now handled correctly.
> 5) remd trajectories can now have numerical extensions of
> arbitrary width, not just %03i.
> 6) Better error checking and more informative error messages
> for remd traj code.
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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