AW: Periodic Box Dimension (WrapAll is on)

From: Norman Geist (
Date: Tue Jan 20 2015 - 00:39:59 CST


Von: [] Im Auftrag von JAVAD NOROOZI
Gesendet: Dienstag, 20. Januar 2015 06:55
An: NAMD list
Betreff: namd-l: Periodic Box Dimension (WrapAll is on)






As far as i know NAMD does not wrap atomic coordinates to the other side of the box until the center of mass of the molecule composed of those atoms pass the boundary.


well as far as I know NAMD wrapps _EVERY_ atom that crosses the boundary, when wrapping is enabled. As this is often not comfortable, people usually turn of wrapping in NAMD and wrap later in VMD with much more options.


The question is what would happen if one specify the periodic box dimension much smaller than the max-min of the initial coordinate file(#.coord)?


In this case center of mass of some molecules stick out the box, does NAMD wrap them to the other side in the very first step?


What if some atoms in a molecule stick out (not the molecule center of mass ) of box?


What happens is that your simulation will very likely crash because of superimposed atoms and very high VDW energy, as for those atoms sticking out of the box now, there’s no space on the other side of the box. Please also notice that wrapping is only a “output” option. The simulation itself will always handle the atoms periodic, if a box is set at all. Seems that you have some critical misunderstanding in some of the fundamentals of molecular dynamics simulation.


What are you trying to do?






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