From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Fri Sep 02 2011 - 11:21:56 CDT
Dear NAMD experts,
I want to move an ion (atomnumbers {1}) along an axis (X axis) while my channel is along Z. I am using "Component distanceZ" as mentioned in NAMD 2.7b3 to do so.
lowerboundary 0.0
upperboundary 4.0
lowerwallconstant 100.0
upperwallconstant 100.0
distanceZ {
main {
atomnumbers { 1 }
}
ref {
atomnumbers { 2 3 4 5 }
}
axis (1.0, 0.0, 0.0)
}
To my understanding, this should change the value of the component e·(r ? r1) from 0 to 4 along X. Also to confine the ion movement along Y and Z, I defined another colvar as below:
lowerboundary -0.1
upperboundary 0.1
lowerwallconstant 100.0
upperwallconstant 100.0
distanceXY {
main {
atomnumbers { 1 }
}
ref {
atomnumbers { 2 3 4 5 }
}
axis (1.0, 0.0, 0.0)
}
I believe this should confine the ion movement in the a plane orthogonal to the X axis (1.0, 0.0, 0.0) defined by the first colvar. However, by checking the trajectory file for the ion positions, it seems that the ion is not moving properly in any of the directions. It's position has changed by 2A along Z right after starting the simulation and fluctuates within 2-3A during the simulation. Along Y, it fluctuates within 1.5A and along X although it is supposed to move within only 4A, it experiences a much wider range (8A). I am wondering whether I misunderstood something in the commands above.
Many thanks,
Parisa
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