VMD-L Mailing List

From: Diego Gomes (diego.enry_at_gmail.com)
Date: Fri Feb 28 2025 - 21:33:00 CST

Hi Edgar, can you share your GRO file? I'm willing to test it on various
platforms.

Try the VMD 2.0 alpha4? It has an updated version of SURF, built with a
newer compiler and libraries.

Be aware it's still an early alpha, crashes may occur.
https://www.ks.uiuc.edu/Research/vmd/alpha/

Friendly,
Diego.

On Fri, Feb 28, 2025 at 4:16 PM Edgar Galicia <galicia.andres_at_gmail.com>
wrote:

> Dear vmd community,
>
> I'm having an issue using the graphical representation Surf. It used to
> work before in Ubuntu 22.04 but since I changed to Debian 12 I get a
> segmentation fault error. Even rendering tested scripts Surf fails. I tried
> in my MBA m2 with sequoia and it works. Would you have an idea of the issue?
>
> These are my specs and error details:
>
> Description: Debian GNU/Linux 12 (bookworm)
> Release: 12
> Codename: bookworm
> arch: x86_64
>
> Info) Finished with coordinate file
> /pool/edgargalicia/GROMACS/KLNT/NO_ANGLE/LEO/solv2_center.gro.
> 0
> Reading 1422 atoms..done
> Probe radius = 3.400
> Constructing solvent-accessible surface ..
> Segmentation fault
> Info) This surface is made with SURF from UNC-Chapel Hill. The reference
> is:
> Info) A. Varshney, F. P. Brooks, W. V. Wright, Linearly Scalable
> Computation
> Info) of Smooth Molecular Surfaces, IEEE Comp. Graphics and Applications,
> Info) v. 14 (1994) pp. 19-25.
> Info) Reading Surf geometry output file...
> Info) Read Surf output file, processing geometry...
> Info) Done.
> prueba.dat
> Info) Rendering current scene to 'prueba.dat' ...
> Info) Tachyon file generation finished
> Info) Executing post-render cmd
> ''/home/edgargalicia/local/vmd/lib/tachyon_LINUXAMD64' -aasamples 12
> prueba.dat -format TARGA -res 1280 720 -o prueba.dat.tga' ...
> Tachyon Parallel/Multiprocessor Ray Tracer Version 0.99.1
> Copyright 1994-2014, John E. Stone <john.stone_at_gmail.com>
> ------------------------------------------------------------
> Scene Parsing Time: 0.1229 seconds
> Scene contains 26167 objects.
> Preprocessing Time: 0.0075 seconds
> Rendering Progress: 100% complete
> Ray Tracing Time: 1.7258 seconds
> Image I/O Time: 0.2083 seconds
> Info) Rendering complete.
> Info) VMD for LINUXAMD64, version 1.9.4a57 (April 27, 2022)
> Info) Exiting normally.
>
> It seems that Surf runs but at some point it crashes. QuickSurf makes no
> issues, but Surf does.
>
> Best,
> Edgar
> 

-- 
Diego Enry B. Gomes, PhD
Department of Physics at Auburn University &
NIH Center for Macromolecular Modeling and Visualization
Leach Science Center - Ste. 3182 - Auburn, AL
dgomes_at_auburn.edu