VMD-L Mailing List

From: Kos (asimplefunguy_at_netscape.net)
Date: Thu Apr 21 2005 - 20:29:21 CDT

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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