From: Sourav Ray (souravray90_at_gmail.com)
Date: Wed May 18 2016 - 07:22:00 CDT
Hello
I am trying to vary the distance between two carbon nanotubes along x-axis.
Additionally, I would like to restrict any rotation, whatsoever, and
translation along y and z axes. I am using "Distancedir" to restrict
translation for both the nano-tubes along y and z axes and "orient" to
restrict rotation with "harmonic" constraint. However, I am not getting the
desired effect. Please find the colvars script below:
colvarsTrajFrequency 10000
colvarsRestartFrequency 10000
colvar {
name cntdis
width 0.1
lowerboundary 12.0
upperboundary 20.0
lowerwallconstant 100.0
upperwallconstant 100.0
distance {
group1 {
atomnumbersrange { 1-364 }
}
group2 {
atomnumbersrange { 365-728 }
}
}
}
colvar {
name orient
width 0.1 # distance between quaternions is from 0 to pi/2, so small
fluctuations are significant
orientation {
atoms {
atomNumbersrange { 1-728 }
enableForces off
}
refPositionsFile ../ref.pdb # Fetch initial positions from this file
}
}
colvar {
name ztrans1
width 0.1
distancedir {
group1 {
atomnumbersrange { 1-364 }
}
group2 {
dummyatom (-6.5,0,0)
}
}
}
colvar {
name ztrans2
width 0.1
distancedir {
group1 {
atomnumbersrange { 365-728 }
}
group2 {
dummyatom (6.5,0,0)
}
}
harmonic {
colvars orient ztrans1 ztrans2
centers (1,0,0,0) (1,0,0) (1,0,0)
forceconstant 10.0
}
metadynamics {
colvars cntdis
hillWidth 2
hillWeight 0.5
newHillFrequency 100
}
Please let me know if someone has any insight regarding the same.
Regards
Sourav
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