From: Vlad Cojocaru (
Date: Thu Jan 12 2017 - 09:02:31 CST

Thanks Hannes, Thanks Giacomo,

.. for your thoughts/advices .. I think I solved the problem ... I
think the problem appeared because originally the openSUSE 42.2 could
not be installed with graphics because of the lack of support for the
Quadro M4000 by the default nouveau driver. I used a workaround to
install in text mode and then compile the NVIDIA driver on top of this
text installation ... With this, actually not only VMD but my entire
graphics were extremely slow. ...It was just more notable on VMD ...

What I did now was to switch to text mode, uninstall the NVIDIA driver
and install it again through the openSUSE 42.2 repositories ... Now, the
speed appears fine (actually is very fast) ..

Giacomo, the reason for having Quadro graphics was because I wanted to
have the 3D vision ... As far as I know on linux this is only possible
with Quadro cards ... If am wrong here or I am missing something, I'd be
grateful for an advice on a setup that works with GeForce and stereo

Thanks again

On 01/12/2017 03:47 PM, Hannes Loeffler wrote:
> Hi Vlad,
> I have a M4000 myself and Dell too (Precision 3620 but would need a
> closer look for the real specs). But I have only noticeable delays on
> start-up and and a bit after quit. But I think I had reported this here
> in a thread of yours.
> Other than that I have no problems. The vmd version is 1.9.3beta1.
> Driver version 370.28, compiled myself with CUDA 7.5. I had some
> strange timeouts when running pmemd, turned out to be the kernel
> version (currently I have 4.7.8).
> Have you tried to change any of those and see if that helps? You could
> also try some other CUDA accelerated software to see if you have
> problems with that.
> Cheers,
> Hannes.
> On Thu, 12 Jan 2017 14:40:45 +0100
> Vlad Cojocaru <> wrote:
>> Dear all,
>> I am experiencing a very awkward problem. I have a new Dell high end
>> workstation (Precision 7810). On this machine VMD (both 1.9.2 and
>> 1.9.3, either compiled from source or downloaded as pre-compiled
>> binaries is extremely slow. Practically, even loading a simple PDB
>> (3000 atoms) and drawing as New Cartoon with resolution 50 almost
>> freezes the VMD window, almost no rotation is possible anymore. This
>> machine has a Quadro M4000 graphics card (see details below). For a
>> comparison my older workstations with exactly same OS, same
>> configurations but with GeForce GTX950 or Quadro K4000 all VMD
>> executables tested (the same as on the new machine) run with no speed
>> issues whatsoever.
>> Has anyone experienced anything similar ? Are there some simple tests
>> one can do to pinpoint the potential issue ?
>> Best wishes
>> Vlad
>> Some details:
>> CPU: Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
>> RAM: 64 GB
>> Graphics: NVIDIA Quadro M4000 (driver 375.26, CUDA 8.0.44)
>> OS:OpenSUSE 42.2 (x86_64)

Vlad Cojocaru, Ph.D., Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]