VMD-L Mailing List

From: FX (fxcoudert_at_gmail.com)
Date: Wed Jan 18 2012 - 06:12:08 CST

Hi all,

I have a strange problem with the "Surf" representation (molecular surfaces). I have a PDB file of a porous material, which when loaded into VMD and switched to "surf" representation:

  -- on my Mac OS 10.7.2, with VMD 1.9 (not the latest beta), works fine
  -- on our x86_64 linux boxes (without CUDA), alternatively does not work (display seemingly random triangles) or crashes VMD as a whole, depending on probe size used; this happens with both versions 1.9 and 1.9.1
  -- on our Windows 7 64-bit box (which has CUDA accelerators), same thing as Linux, both with 1.9 and 1.9.1

I cannot make any sense of that. I know that the "surf" code is not the most stable algorithm, but that's very impressive crashing rate. Moreover, I thought there was a new CUDA-based code for calculation of molecular surfaces (the "surf" representation) in 1.9.1, and so I expected it to work fine on the Windows system (which detects the graphic card fine, and states that CUDA accelerators are present).

So, how do I debug this? Are any of my assumptions wrong? How could I get the CUDA version of the code to run on Windows (hoping it is more stable that the external SURF program)?

Many thanks in advance,
FX Coudert