From: Prskalo, Alen-Pilip (
Date: Wed Jul 21 2010 - 08:42:42 CDT

Hi Ian,

thank you very much for the fast reply.

First off all, I forgot to mention, I had a problem of my .pdb file having more than 99.999 atoms, so VMD didn't read them well. This bothered me for a while, I read some posts here I tried to solve it by maybe using other data formats etc. Then a colleagues told me, he simple uses the same number for all atoms. It seemed to be very simple to be true, but it works perfectly as I tested it few hours ago. I even wanted to make a post here and to make a joke if I can number the atoms using hexadecimal scale ;-) but with 5 digits max that would make a jump from 100.000 to 1.000.000 which is also not very much. So for everyone having similar problems, simple do not count atoms and use a dummy index, VMD counts internally anyway.

So, finally as a reply: I have a standard Quad Core, nothing special. The intended upgrades did not go in the way of buying a new PC, although would be very interesting to see how it works. I simply wanted to push the existing PC to a max.

I use a HPC cluster for the calculations and I am still considering where to do the post processing, either locally or on one of the clusters. Depending on the performance and costs I will try to make the best decision.
My first test today was a MD simulation of a simple nano indentation, I had slightly over 1.000.000 atoms and visualized it as 100 single frames, that means I had a large (~ 7 GB) movie.pdb containing all single frames in it.
On a cluster, running interactive job on a single 4 core CPU, with no CUDA on it, it took VMD about 2.5 minutes to load all frames and playing directly from VMD was quite nice, but not really fluent.

I informed myself a bit (actually I takes me meanwhile 2 hours to write this post, in between bothering my HPC colleagues what kind of hardware we have), I actually can use a one of the visualization nodes for running VMD. There I have 2 Quad Cores with 16 GB memory and Nvidia graphic card with OpenGL support (I must admit I am new to graphic card topic, so im telling you what I interpreted on the phone ;-) As I understand it, starting an interactive job on such a node would allow me to use it as it was here, my bothering was especially which graphic card is used in this case, the super mega one on the node or my onboard locally. But as I was explained, I can use the whole power of the node, as long there is enough bandwidth.

@ Axel: thank you also for the explanations, your email came after I started replying to Ian, so I am simply adding some lines.
My questions is: what other file format instead of .pdb should I use? I saw something about .xyz files, which should be more simple, but could not explain myself yet what a trajectory file which is also mentioned in relation with VMD. I have a co called checkpoint file, that means for each simulation time I get a file containing all atom coordinates, velocites and potential energies. The form is

"atom_number atom_type atom_mass x-coord y-coord z-coord v_x v_y v_z E_pot"

What would you say is the best format I should use

Kind regards


Dipl.-Phys. Alen-Pilip Prskalo
Institut für Materialprüfung, Werkstoffkunde und Festigkeitslehre IMWF
Universität Stuttgart
Pfaffenwaldring 32
70569 Stuttgart
Tel: +49 711 685 52579
Fax: +49 711 685 62635

From: Ian Stokes-Rees []
Sent: Mittwoch, 21. Juli 2010 14:08
To: Prskalo, Alen-Pilip
Subject: Re: vmd-l: PC suitable for visualisation of large systems, maximum namuber of atoms in a .pdb file

On 7/21/10 3:40 AM, Prskalo, Alen-Pilip wrote:
I'm new in the VMD community, used Rasmol before. I am simulating systems of ~1.000.000 atoms in each frame and I intend to make nice videos later on. So it is obvious that I will have an enormous .pdb file containing large number of atoms AND frames to make the video look fluent. My question is: what is the best PC to do it? I do have a bit money on the side to upgrade my 4 Core, 4GB RAM PC, but how? First idea is of course to by extra RAM, to go to 8 GB or even 16 GB. What about the graphic card, presently I have only onboard graphics, would a good graphic card make the loading and rotation easier and if, how exactly (from the technical stand point).

I don't have direct experience with this, but from my indirect experience you would probably be well suited to purchase one of the new 8 or 12 core per CPU AMD systems which can get you 32 or 48 cores in a single box, include a recent nVidia CUDA 3.0 graphics card (a Tesla would be best, but an OEM model would probably work alright as well), and then buy at least 16 GB of RAM, if not more. From what I understand, you can put in as many Tesla cards as your system can handle and VMD will pick them up and use them all.

Are you running the simulation on the computer, or is the simulation running on a separate MD cluster? If it is running somewhere else, you could make do with fewer CPUs. If it is running on the new computer you are going to get, you should aim for the 48 core AMD system. Here in the US you can get such a system for about $7k, or "fully loaded" (fast disks, lots of RAM, etc. etc.) for under $10k.

I am very interested to hear what other people recommend.