Umbrella Sampling

From: Buddhadev Maiti (chebm_at_langate.gsu.edu)
Date: Tue May 17 2011 - 21:52:38 CDT

Dear NAMD Users,
I am trying to prepare input files for umbrella sampling using NAMD-2.7 with colvar option. But I am not getting clear information in NAMD-2.7 manual. Could you please help me about Distance.in file. I am pasting below. Regarding centers, which value do I need to choose. The initial distance between the two groups is 5.77 Angstrom. Is it necessary to keep width, lowerwallconstant and upperwallconstant.
Have a nice day,
Thanks,
Maiti

Distance.in:

Colvarstrajfrequency 1000
Colvarsrestartfrequency 1000
colvar {
name ProjectionZ
lowerboundary 5.52
upperboundary 6.02
distanceZ {
main {
atomnumbers { 6633 6640 6654 6661 6675 6694 6716 6735 }
}
ref {
atomnumbers { 1681 1703 1719 1730 1742 1763 1778 1795 }
}
axis (-0.50, -0.56, -0.64 )
}
}
harmonic {
colvars ProjectionZ
centers 5.77
forceConstant 10.0
}

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