From: Per Jr. Greisen (pgreisen_at_gmail.com)
Date: Tue Oct 23 2007 - 12:49:45 CDT
Hi,
I am trying to pull to atoms away from each other using the ABF module in
NAMD. The files which should include the forces as well as the energies only
have zeros within it:
# xi A(xi) av_force n_samples
3.700 0.0000 0.0000 0
3.900 0.0000 0.0000 0
4.100 0.0000 0.0000 0
4.300 0.0000 0.0000 0
4.500 0.0000 0.0000 0
4.700 0.0000 0.0000 0
4.900 0.0000 0.0000 0
5.100 0.0000 0.0000 0
5.300 0.0000 0.0000 0
5.500 0.0000 0.0000 0
5.700 0.0000 0.0000 0
5.900 0.0000 0.0000 0
6.100 0.0000 0.0000 0
etc etc...
I have tried to add the writeXiFreq to debug the problem(this doesnt work)
My input is
source TCL/abf.tcl
abf coordinate distance
abf abf1 286
abf abf2 778
abf outputFreq 500
# Width of bins in which forces are collected
abf dxi 0.2
# Minimum distance below which no sampling is performed
abf xiMin 3.60
# Max. distance above which no sampling is performed
abf xiMax 8.0
abf outfile mt.dat
# Number of samples prior to ABF
abf fullSamples 500
abf inFiles {}
abf distFile test.dist
# Length over which force data is averaged
abf dSmooth 0.4
# write the frequency
run 800000 ; # 400 ps
What is wrong and how to fix this - thanks in advance
-- Best regards Per Jr. Greisen
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