VMD-L Mailing List

From: Chris Neale (candrewn_at_gmail.com)
Date: Mon Jan 04 2021 - 19:47:17 CST

Dear John:

thank you for your help.

Using vmd 1.9.3 and the lib/ and include/ directories from my Amber18
installation as the source netcdf, I was able to build the netcdfplugin.so
once I modified the Make-arch file to have "NETCDFLDFLAGS = -lnetcdf " in
the OPENPOWER section. Then adding the same Amber18 lib/ directory to my
LD_LIBRARY_PATH, and setting VMD_PLUGIN_PATH to the OPENPOWER/molfile
directory from VMD, I was able to get gromacs trjconv to read amber netcdf
trajectories on summit.

Thank you,
Chris.

On Thu, Dec 31, 2020 at 10:12 AM John Stone <johns_at_ks.uiuc.edu> wrote:

> Chris,
> To compile the AMBER plugins for NetCDF requires first compiling
> the NetCDF library itself. I hadn't done this since up to this point
> nobody had asked for AMBER support on Summit, but if you're working
> with large AMBER trajectories there it shouldn't be too difficult to
> achieve this. Have you compiled (or do you have a pre-compiled) NetCDF
> library? If so, compiling just the AMBER plugin with the NetCDF library
> is pretty simple. If not, then that's really the first step one has to
> take, and from there we can compile VMD and/or the AMBER plugin itself
> against the NetCDF libs. If you haven't started on this, then let me know
> and I'll see if I can take a stab at it.
>
> Best regards,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sat, Dec 26, 2020 at 10:49:32AM -0700, Chris Neale wrote:
> > Hello,
> >
> > I am trying to use the VMD plugins on the OLCF/ORNL cluster Summit to
> > permit gromacs to load in Amber format NetCDF files. However, the CPUs
> are
> > IBM???s POWER9 there and I???ve had trouble compiling from source or
> figuring
> > out which precompiled files to download. The LINUX downloads have plugins
> > that are not recognized by gromacs on this architecture, and the
> openPOWER
> > 1.9.3 download is missing a netcdf plugin. I see there???s a NAMD/VMD
> paper
> > out on Summit usage, so I am hoping that there is some simple option
> here.
> >
> > Thank you,
> > Chris.
>
>
> --
> 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/
>