From: Axel Kohlmeyer (
Date: Mon Nov 08 2010 - 12:38:46 CST

On Mon, Nov 8, 2010 at 12:38 PM, Prskalo, Alen-Pilip
<> wrote:
> Hi all,
> i have allready posted a few times here, I got help quite fast, so I'll try
> it again.
> Firstly, i indent to by a Nvidia workstation, among other software i
> especially indend to run VMD on it. Components should be as following: 2
> Intel 6-Cores, around 32 GB RAM, Nvidia mainboard with SLI, and most

> important, graphics card. As stated, I'll take SLI, so if one GPU is to
> little, I'll take the advandage of havind the other one also. I still

not sure, if there actually is a benefit from SLI on linux /w opengl.
a colleague tried it and didn't see anything.

> have some doubts, either to got with Nvidia Quadro FX 5800 4 GB or Nvidia
> GeForce GTX 480, I must addmit i dont know the difference between the Quadro
> and GeForce card so I'll take the best one of both models. Quadro is
> around 2500 Euro and GeForce arround 350 Euro, so the equation seems to be
> very simple. The reason why i doubt the Quadro card (besides the price ;-)
> is the fact that a colleaque of mine bought one workstation with a Quadro FX
> 5800 in it and was dissapointed, so was I, i tried to rotate a a system
> sonsisting out of 1 000 000 atoms in PDB file format. As long as i stayed in
> line representation, everything worked fine, but as soon as i used CPK, the
> PC hanged, i could not move the system as i wished, i had to wait for

this will happen with _any_ card. the Quadro FX5800 is pretty powerful.
its graphics performance is roughly equivalent to a GTX 280. so the
GTX 480 should be faster, but also _much_ hotter.

to get better performance on high end graphics cards you should
enable GLSL. this way, your CPU only needs to compute the centers
and radii of spheres and GPU does the rest. that being said. for a 1M
atom system, you will alway have the lines or points rep be much faster.

i regularly visualize systems that are up to 10x larger and always use
points or lines at point size 5 or larger together with depth cueing rather
than GLSL as that is the only way to operate smooth enough. rendering
those systems on the screen with a more detailed rep is more distracting
than helpful, IMO. that being said, if i look at subsets of the system, i
certainly use the higher quality visualization reps.

> minutes until a rotation was performed. Or did i expect to much, could
> someone tryed to to this on their own PC with a good graphics card and tell
> me if i works.

you are expecting far too much. you should also consider that with
1M atoms, you don't have much room for each atom, so what is the
point to spend a lot of computing effort on a sphere or cylinder if
that results in only a few pixels.

> Secondly: would a a Tesla card accelerate VMD graphics if I used it for
> visualisation only and dont perform any acctual GPU calculations? So, to
> have a Tesla and a Quadro for instance.


> Third question: I perform MD calculations on a HPC cluster, the output i get
> are checkpoint files, basically snapshots of the system for specific time
> step. The file format is of following: 10 columns (atom number, atom type,
> mass, x, y, z, v_x, v_y, v_z, E_pot). For a a smooth visualisation with VMD
> i transform each file into a PDB file format and then glue them together
> with an "END" inbetween each frame. This is recognized by VMD as a time
> scale so i can run it as a movie. The problem is offcourse that i have a
> huge single file, depending on the number of atoms and number of individual
> frames, so VMD gets very slow. As i was told by Axel Kohlmeyer as a respond
> on to my previous posts, it is due to the fact that PDB is first of all a
> text format, having the data into binary format would improve the
> performance. VMD uses some kind of a start configuration and a trajectory
> file, both in binary format. Could someone explain me how i get my bunch of
> files into this binary format(s).

write a converter, or have your MD code output .dcd or .xtc directly,
or write an interface to the VMD molfile plugin library.


> I thank you all in advance for any help i get.
> Regards
> Alen Prskalo
> Dipl.-Phys. Alen-Pilip Prskalo
> Institut für Materialprüfung, Werkstoffkunde und Festigkeitslehre IMWF
> Universität Stuttgart
> Pfaffenwaldring 32
> 70569 Stuttgart
> Tel: +49 711 685 62579
> Fax: +49 711 685 62635
> Email:
> Email:

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.