From: Bala subramanian (bala.biophysics_at_gmail.com)
Date: Sat Nov 19 2016 - 08:18:57 CST
Friends,
My objective is to restrain an ion-A within a Z-distance of 6.5Ang from
ion-B. I defined the colvar as below. I dnt apply any other bias on ion-A
colvar {
name LONGI
width 0.5
upperboundary 0.0
lowerboundary -6.5
lowerwallconstant 100.0
upperwallconstant 100.0
distanceZ {
main {
atomnumbers { 16628 } ; ion-A
}
ref {
atomnumbers { 16625 } ; ion-B ( Z of B > Z of A)
}
axis ( 0.0, 0.0, 1.0 )
}
}
When i analysed the colvar.traj, i see that the distanceZ varying -6.82 to
-4.10. I wonder how when i fix the distanceZ to be within -6.5Ang, it
increase up to -6.82 ?. Is it normal ?. Do i need to use any other criteria
to achieve distanceZ to be strictly within -6.5.
-- C. Balasubramanian
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