AW: TclForces and efficient PBC corrections

From: Norman Geist (
Date: Tue Nov 12 2013 - 01:19:01 CST

1. I don't think so.


2. To get the clostest periodic distance between two atoms I usually
do (pseudo code):


$xd = pmodulo($x1-$x2+$boxX/2,$boxX) - $boxX/2

$yd = pmodulo($y1-$y2+$boxY/2,$boxY) - $boxY/2

$zd = pmodulo($z1-$z2+$boxZ/2,$boxZ) - $boxZ/2

$dist = sqrt(pow($xd,2) + pow($yd,2) + pow($zd,2))


Make sure to use the pmodulo "positive arithmetic remainder", standard
module can't do negative numbers.


3. IMHO tcl don't mind. Check if you can improve parts of your script.


Norman Geist.


Von: [] Im Auftrag
von Morgan, Brittany
Gesendet: Montag, 11. November 2013 19:03
Betreff: namd-l: TclForces and efficient PBC corrections


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


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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