AMBER Archive (2009)

Subject: RE: [AMBER] bintraj and amber 10

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Apr 23 2009 - 08:31:08 CDT

Hi Naser,

The bintraj file is written as a binary file so doesn't have a number of
digits in the same fashion as the ASCII mdcrd file. It does however, have a
number of significant figures as defined by the precision of the floating
point numbers written to the file.

I believe that the coordinates are written as a series of single precision
floating point numbers (although I might be wrong here and it could be
double precision - I don't have time to check right now).

The format is described in appendix E of the AMBER 10 manual.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Naser Alijabbari
> Sent: Wednesday, April 22, 2009 6:05 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] bintraj and amber 10
>
> 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 |
> >
> > Note: Electronic Mail is not secure, has no guarantee of delivery,
> may not
> > be read every day, and should not be used for urgent or sensitive
> issues.
> >
> >
> >
> >
> >
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