VMD-L Mailing List

From: Thomas Evangelidis (te8624_at_mbg.duth.gr)
Date: Fri Dec 26 2008 - 16:01:33 CST

> a 1000 frame trajectory file can be easily generated, even on a small
> machine. you only need to run a small system...
  Now that I gave it a second though I could just append a small
trajectory to itself multiple times with catdcd. However none of the
trajectories I possess contains carbonhydrates or lipids. It would be
interesting to see how my code can handle such cases.

> is there are specific reason why you'd need a production quality run?
>
> it would also help, what kind of plugin you are working on and what
> specific properties you'd need in the trajectory.

My plugin can keep only the macromolecule and a given number of closed
waters and other heterocompounds, and removes the rest from every
frame. In other words truncates the trajectory. Do you see now why I
need a big trajectory?