VMD-L Mailing List

From: Jonathan Phillips (pcxjp3_at_nottingham.ac.uk)
Date: Fri Jun 14 2013 - 16:53:33 CDT

Hi,
I'm really confused. I've been running simulations in NAMD2.9, and analysing them in VMD1.9.1. I've been using a tetrahedral box and a langevin piston.
According to this old email (http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/4990.html) the dcd files should contain the unit cell information.

When I look at my simulations there are regions where the box appears to overlay with the '+Y' box (found under graphical representations, periodic) - after a while of searching I found a pair of TIP3 molecules which were stupidly close to one another - one in 'self' the other in '+Y'. Some TIP3 molecules are practically inside alpha helices. There are also some gaps which should be covered by water molecules from another copy of the box, but aren't. And the faces of the boxs are offset with respect to one another.
I've checked my NAMD code, and I can't see any stupid mistakes (pretty certain I do actually have an octahedral box), which means it's probably VMD's fault (or my fault for not knowing how to use VMD).

Does anybody know what's going on? Do I need to use a special command to get VMD to read the periodic box information correctly? Am I in fact doing something wrong in NAMD? Is there another program that will move the TIP3s so my protein is in the centre - so I could run it before running VMD?

Any help would be appreciated,
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