TclForces and efficient PBC corrections

From: Morgan, Brittany (
Date: Mon Nov 11 2013 - 12:02:52 CST

Hi All,

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.

Brittany Morgan

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