VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 31 2020 - 11:12:14 CST

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
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