From: 宋瑞珩 (141130085_at_smail.nju.edu.cn)
Date: Tue Nov 29 2016 - 04:28:21 CST
Dear all
I used the RMSD as a reaction coordinate to calculate the potential surface of a conformation change. I set the RMSD boundary ranging from 3.4 to 3.6 and the lower wall constant to be 100, as the tutorial said. However, I found the RMSD value in the output file went beyond my constraints and decreased to 3.1. I tried to increase the wall constant to 100000, but it still did not work. Does anyone know how to solve this problem? Here is my input file:
Colvarstrajfrequency 100
Colvarsrestartfrequency 1000
colvar {
name RMSD
width 0.01
lowerboundary 3.4
upperboundary 3.6
lowerwallconstant 100.0
upperwallconstant 100.0
rmsd {
atoms {
atomsFile 3.5.pdb
atomsCol B
atomsColvalue 1.00
}
refPositionsFile ref.pdb
refPositionsCol B
refPositionsColValue 1.00
}
}
abf {
colvars RMSD
fullSamples 500
hideJacobian
}
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