VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jan 18 2012 - 08:00:54 CST

On Wed, Jan 18, 2012 at 7:12 AM, FX <fxcoudert_at_gmail.com> wrote:
> 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)?

what you are looking for is the "QuickSurf" representation.
Surf is unchanged.

axel.

>
> Many thanks in advance,
> FX Coudert 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.