RE: visualizing and analyzing long simulation

From: Deng, Jinxia (Nancy) (
Date: Mon Oct 10 2016 - 10:51:42 CDT

Instead of catdcd, you can use stride option, say 10 or 100 to take every 10th or 100th frame of the original dcd file.

Hope this helps,

From: Dhiraj Srivastava []
Sent: Monday, October 10, 2016 11:42 AM
Subject: namd-l: visualizing and analyzing long simulation

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   I have dcd file with 100000 frames which even after stripping off all the water is more than 30 gb in size. Its difficult to load this much of data in VMD. My question is, how everyone normally look at these data? should I use catdcd to get rid of most of the frames and lets say save every 100th frame or so?



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