VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jan 04 2019 - 11:43:06 CST

John,

the LAMMPS netcdf files are supposed to be compatible with amber. it
uses Conventions = AMBER. i can easily produce example files. source
code is available here:
https://github.com/lammps/lammps/blob/master/src/USER-NETCDF/dump_netcdf.cpp#L222

from what i can tell, it doesn't even get to the point of checking
which conventions it follows, but fails in the nc_open() function.

which version of netcdf do you compile the plugin/VMD with?

axel.

On Fri, Jan 4, 2019 at 12:34 PM John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> The NetCDF reader in VMD currently understands NetCDF files written
> by AMBER, MMTK, and some others, but as of yet there is no reader for
> LAMMPS data there. If someone has documentation about LAMMPS NetCDF
> files and some example files, I would be interested in implementing
> the required changes to add the necessary support.
>
> Best,
> John
>
> On Wed, Jan 02, 2019 at 12:52:35AM -0500, Axel Kohlmeyer wrote:
> > On Tue, Jan 1, 2019 at 1:40 AM LIGESH B <ligeshkannur178_at_gmail.com> wrote:
> > >
> > > Dear Users,
> > > I have done a simulation of polymers in LAMMPS. The output file format is netcdf type (file.nc) but when I try to load it VMD using Ubuntu OS. It is showing a error as could not read the file.
> >
> > > Why it is showing this error?
> >
> > impossible to say from remote. possibly, because it cannot read the
> > file, or the format is not compatible.
> >
> > > What may be the possible solution?
> >
> > use a different file format?
> >
> > axel.
> > >
> > > Thanks in advance
> > >
> > > -Ligesh
> > >
> >
> >
> > --
> > Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> > College of Science & Technology, Temple University, Philadelphia PA, USA
> > International Centre for Theoretical Physics, Trieste. Italy.
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.