From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Wed Nov 24 2010 - 16:11:16 CST
Dear NAMD users,
I am a little confused with the definition of "abf coordinate zCoord-1atom" in tutorial when using ABF.
I know that "zCoord-1atom" corresponds to the distance separating an atom and a group of atoms along the z-direction of Cartesian space. My system consists of an ion moving in a channel and I want it to move just along Z not x and y directions. I looked throughly in the mailing list and came up with these two replies which are not in agreement ( at least I cannot understand it):
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/6156.html
and
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/9270.
The first one assumes there is no need to constrain ion movement along any other directions perpendicular to Z while the second one, tells me that the only way to guarantee this is to constrain the movement along x and y.
I tried the first one as below and it seems the ion is moving everywhere.
# ABF SECTION
source /opt/namd/2.6/32bit/lib/init.tcl
package require abf
abf coordinate zCoord-1atom
abf abf2 { 781 }
abf abf1 { 89 284 479 674 122 707 317 512 }
abf dxi 0.2
abf xiMin 0
abf xiMax 9.9
abf forceConst 10.0
abf outFile dna.dat
abf fullSamples 800
abf distFile dna.dist
abf dSmooth 0.4
abf applyBias yes
abf historyFile dna.history
run 2000000
Thanks,
Parisa
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