From: Prskalo, Alen-Pilip (
Date: Mon Nov 08 2010 - 11:38:22 CST

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 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 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.

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).

I thank you all in advance for any help i get.


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