From: Kong, Ren (rkong_at_houstonmethodist.org)
Date: Tue Aug 06 2013 - 11:06:41 CDT

Dear NAMD users,

I have run NAMD for my system with wrapAll parameter on.
When I used VMD to observe the trajectory file, I found that there were some atoms with big jump in coordinates. So I used the "pbc unwrap" in tcl/tk to get a trajectory with continuous coordinates.
But I found that the water molecules in the active site of the protein disappeared after unwrap. Which should I use to do the analysis? The trajectory before or after unwrap? I want to analysis the water molecules in the active site. Are the water molecules really inside the active site during the simulation or it is just the effect of periodic box?

Ren Kong Ph.D.

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