VMD-L Mailing List

From: Kos (asimplefunguy_at_netscape.net)
Date: Fri Apr 22 2005 - 11:00:38 CDT

Hi John,
thank you for your answers which
cover the major part of my questions.
Now we need to try them
to see how VMD works for us (great sci-SW).

Kos

John Stone <johns_at_ks.uiuc.edu> wrote:

>
>Kos,
> VMD doesn't have any limits on the number of trajectory frames you
>can load other than that you have enough RAM to store them all. It's
>clear from what you've said so far that you're unaware of the RAM
>requirements to load large trajectories in VMD. I've loaded 32GB
>trajectories on machines that have enough memory, so believe me,
>it can be done. But, if you don't have the memory, you will have
>to either load only a subset of frames, or you'll have to process them
>with your scripts one-frame-at-a-time. I have several suggestions below
>which I hope will clarify things to you and others:
>
>1) If the DCD file size on disk is larger than your computer's RAM,
> you won't be able to load all of it into VMD at once.
> i.e. if you have 512MB of RAM, but a 2GB DCD file, there's no way VMD
> will load it in its entirety. You will have to load a subset of frames
> or process them one-at-a-time (see below).
>
>2) If you know you don't have enough memory to load the entire file,
> you will have to load a subset of frames.
> If you're loading the DCD file for visualization, use the "stride"
> parameter in the "Frames" area of the molecule file browser window
> (file loading window) to skip an appropriate number of
> frames to bring it within the amount of RAM your machine has.
> This way you can visualize the entire trajectory, but you will be
> skipping frames as you watch. If you have 512MB of ram, but want
> to view a 2GB DCD file, you need to set the "stride" value to at
> least 4, best 5 to be safe.
>
>3) If you're using VMD purely for analysis, you can run it in text mode
> with 'vmd -dispdev text'. Also, for simple analyses that don't require
> _all_ of the trajectory frames to be loaded at once, you should be using
> the "BigDCD" script in the VMD script library, which is an
> easy-to-use method for doing analysis on trajectories that are FAR
> too large to fit into physical memory. The script is located here:
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/bigdcd/
>
>4) If you want VMD to load the DCD file as fast as possible, select
> the "load all at once" option in the "Frames" area. This will cause
> VMD to spend 100% of its CPU cycles loading the trajectory file before
> continuing, rather than the default behavior which is to load the
> trajectory file in the background so you can begin viewing it immediately.
>
>Enjoy,
> John Stone
> vmd_at_ks.uiuc.edu
>
>On Thu, Apr 21, 2005 at 09:29:21PM -0400, Kos wrote:
>> Hi,
>>
>> We analyze large trajectory files with SALT IONS, WATERS, APROTININ (30000 atoms) produced by NAMD. We run them in a linux cluster and we analyze them in dual Intel Xeon system with VMD (Windows XP) using Exceed- (X-Windows). As long as the .dcd files are small around 300MB we didn't encounter problems analyzing them with X-VMD(Exceed) or even ftp the .dcd files in the Windows PC from Linux OS and analyze them directly with VMD for Windows.
>>
>> The problem is that when we analyze large 1ns .dcd file the X-VMD dissapears/crashes and can't read. When we transfer the files to Windows PC and try VMD there error for the trajectory file:'can't load , can't read the time etc'. Are there limitations in VMD? I noticed that for 10000frames is very slow to load and crashes.
>>
>> Is CHARMM an alternative solution to these problems and can treat large files faster because doesn't need graphics? A general question: Is CHARMM a more advanced package for MD analysis although not so friendly and how does compare in the postprocessing part with VMD?
>>
>> kos
>>
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>--
>NIH Resource for Macromolecular Modeling and Bioinformatics
>Beckman Institute for Advanced Science and Technology
>University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>

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