VMD-L Mailing List

From: James Kress (jimkress_58_at_kressworks.org)
Date: Sun Dec 04 2016 - 20:40:39 CST

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

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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 

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