From: 宋瑞珩 (141130085_at_smail.nju.edu.cn)
Date: Wed Dec 14 2016 - 05:45:28 CST
Dear all
I used the RMSD as a reaction coordinate to calculate the potential surface of a conformation change. I found the free energy decreased steeply with the reaction coordinate(the gradient is about -100kcal/A, this is quite a large value). However, the previous MD simulation in NPT ensemble revealed that the initial state(rmsd=1) had a lower energy than the final state(rmsd=4), and the energy difference between the two states was about 100kcal/mol. I have no idea about the paradox. Can anyone give some suggestions? Here is my input file:
Colvarstrajfrequency 100
Colvarsrestartfrequency 1000
colvar {
name RMSD
width 0.01
lowerboundary 1.0
upperboundary 4.0
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
}
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