From: Morgan, Brittany (Brittany.Morgan_at_umassmed.edu)
Date: Mon Nov 11 2013 - 12:02:52 CST
I use TclForces and I need to correct for periodic boundary conditions. I have procedures which correct for PBC brute force, but I'm having serious performance issues when I turn them on (the time required more than doubles).
Can anyone tell me if:
1. For the scalar distance, does "getbond <coor1> <coor2>" return a distance corrected for periodic boundary conditions?
2. Is there a built-in way to obtain the vector distance between two positions, corrected for periodic boundary conditions? Or does anyone know of a resource for doing more efficient calculations in Tcl?
3. Is the IBVERBS version of charmrun faster when using TclForces?
I didn't have serious performance issues with my PBC corrections previously, but I've recently started working on a new cluster and this problem has appeared. Previously, I was using NAMD 2.9b2, but IBVERBS is not currently working on the new cluster. I've been using NAMD 2.9-multicore instead.
Any suggestions would be much appreciated.
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