VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Dec 04 2016 - 21:25:34 CST

Jim,
  The NetCDF is included with the Linux and MacOS X builds by default.
If you just select the .nc file in the file browser in VMD, it will
recognize it as a NetCDF file, and it will look at the contents, determine
that it's an AMBER trajectory and do the right thing from there. You shouldn't
have to do anything since your file has the ".nc" suffix. If it had been named
with a different suffix, you might have had to tell VMD it's a NetCDF file
by selecting the file type in the load menu, but that should not be necessary
in this case.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Dec 04, 2016 at 09:40:39PM -0500, James Kress wrote:
> John,
>
> Thanks! I'll try the Linux version of VMD. Is there a link to directions
> on how to implement and use the NetCDF plugin?
>
> Jim
>
> James Kress Ph.D., President
> The KressWorksR Institute
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> -----Original Message-----
> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> Sent: Saturday, December 03, 2016 11:48 PM
> To: James Kress <jimkress_58_at_kressworks.org>
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: AMBER trajectory visualization
>
> James,
> The .nc file is an AMBER trajectory stored in a NetCDF file.
> I'm not sure about the .topo topology file, that's not familiar to me,
> perhaps that's what they used to call a "PARM" file?
>
> The Unix/Linux and Mac versions of VMD contain a NetCDF plugin that can read
> the AMBER .nc files.
>
> Unix compilation of the NetCDF plugins has historically been
> straightforward, particularly the older NetCDF 3.x library, which is all
> that's needed for the existing AMBER formats supported by the NetCDF plugin.
>
> In principle, the VMD NetCDF plugin itself should compile fine on Windows,
> however this requires matching the version of the MS compilers used for VMD
> and NetCDF against each other, and thus far we haven't had a VMD build that
> matched what the pre-built NetCDF libs were built with.
>
> I have looked at compiling the NetCDF-C libraries for Windows, but the
> procedures for building them are complex since they now have dependencies on
> HDF5 as well, and again, the last time I went for it,
>
> I discovered that we were using compilers that were (at that time) too new
> for NetCDF/HDF. Looking at the latest NetCDF library it appears they are
> now using MSVS 2012, which is a big step forward since I last looked. The
> issues with dependencies on HDF5 etc still remain, but it's the compiler
> versions that are more critical due to sensitivities there with other
> libraries and runtimes we link against for core parts of VMD. Here's the
> NetCDF page of interest that describes their existing binary release and
> source compilation methodology:
> http://www.unidata.ucar.edu/software/netcdf/docs/winbin.html
>
> Cheers,
> John
>
> On Sat, Dec 03, 2016 at 09:33:16PM -0500, James Kress wrote:
> > I have two files from an AMBER simulation, traj.nc and vacuo.topo
> >
> > How do I use VMD to visualize these files? traj.nc is a binary file
> > containing the trajectory information. vacuo.topo is the associated
> > AMBER topology file.
> >
> > Thanks.
> >
> > Jim Kress
>
> --
> 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/ 

-- 
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/