VMD-L Mailing List

From: Marc Q. Ma (qma_at_oak.njit.edu)
Date: Fri Apr 22 2005 - 09:15:17 CDT

Kos,

Some sugestions:

1. Use a computer system with larger memory. 1, 2, 4GB. The larger, the
faster.

2. When you produce the trajectories, save less frequently, say every
1ps per frame. Do not do it every 10fs per frame.

3. Or you may save as often as you wish (for whatever purposes), but
you need a DCD_SPLITTER program to split the DCD files -- say save
1/10 of total number of frames to new files, and load these new files
for analysis.

4. This maybe a nice feature, however, VMD still does not have: when a
user load a dcd file, let the user control how many frames to load, how
many frames to skip -- similar to what is provided for "Delete Frames"
after all frames are loaded. This way, researchers can quickly check
the trajectories without loading all frames.

All above is related to allowing VMD to have ample computer memory to
show graphics.

John: Do you think (4) is a good feature to be added to VMD? I think it
will be cool. Currently, my group is using Suggestion #2. This is not
the best solution since the more we save, the more we can infer from
our simulations.

Marc
On Apr 21, 2005, at 9:29 PM, 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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