Force constant for Umbrella Sampling

From: Buddhadev Maiti (chebm_at_langate.gsu.edu)
Date: Mon Feb 14 2011 - 19:19:02 CST

• Next message: hamze rahimi: "problem with MD"
• Previous message: Buddhadev Maiti: "ABF calculation using RMSD"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Dear NAMD Users,
I am performing Umbrella sampling using NAMD-2.7 version. Basically I would like to know whether in this calculations, as far as the force constant is concerned, the selected part of the different atoms can be regarded as a single effective "atom" or the force constant refers to individual atoms inside each selected region. Also, I would like to know what is the appropriate value of the force constant. Also please suggest me if any problem in Distance.in file, it will be great help for me.
Have a nice day,
Thanks,
Maiti

Distance.in:

Colvarstrajfrequency 1000
Colvarsrestartfrequency 1000
colvar {
name GRrmsd
width 0.1
lowerboundary 19.955
upperboundary 21.955
lowerwallconstant 100.0
upperwallconstant 100.0
rmsd {
atoms {
atomsFile 1.pdb
atomsCol O
atomsColValue 1.0
}
refPositionsFile ep.pdb
refPositionsCol O
refPositionsColValue 1.0
}
}
harmonic {
colvars GRrmsd
centers 20.955
forceConstant 10.0
}

• Next message: hamze rahimi: "problem with MD"
• Previous message: Buddhadev Maiti: "ABF calculation using RMSD"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:38 CST