From: Norman Geist (norman.geist_at_uni-greifswald.de)
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.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Morgan, Brittany
Gesendet: Montag, 11. November 2013 19:03
Betreff: namd-l: TclForces and efficient PBC corrections
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.
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