From: Seibold, Steve Allan (stevesei_at_ku.edu)
Date: Wed Mar 16 2022 - 08:21:47 CDT
Hello
I am pulling a peptide from metallic surface using NAMD. I am comparing the process using SMD and Colvars. I have found that I have to use a substantially higher (over 10 times) force constant with Colvars than I do using SMD to remove the peptide from the surface.
My concern is that I am doing something incorrect in setting up my Colvars script shown below. I would appreciate any insights..
Thanks, Steve
colvar {
name Translocation
width 1.0
lowerboundary 7.50
upperboundary 17.512
lowerwallconstant 100.0
upperwallconstant 100.0
outputvelocity on
distanceZ {
main {
atomnumbersrange { 1-90 }
}
ref {
atomnumbers { 902
}
}
axis ( 0.0, 1.0, 0.0 )
}
}
harmonic {
name Y
colvars Translocation
centers 13.0
forceConstant 5.0; # 500 * 0.1^2 = 0.1
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