From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Mon May 15 2017 - 04:18:28 CDT
Dear all,
I am seeing a problem specific to NAMD 2.12. When applying a harmonic
restraint (test steered MD simulation) on a "distanceInv" collective
variable, the variable is not changed during the simulation (despite of
targetCenters set to 40, the colvar stays around its initial value
(6.8-7.2) throughout the simulation, see configuration file below).
Exactly the same test simulation runs absolutely fine with NAMD 2.10
(currently I am testing with 2.11 as well).
The regular "distance" colvar works fine. Has anybody else experienced
this ?
If you need further information/files off the list please let me know
Best wishes
Vlad
colvarsTrajFrequency 100
colvar {
name DistInv-PouS
width 0.5
distanceInv {
exponent 10
group1 {
atomsFile colvar_ref.pdb
atomsCol B
atomsColValue 1.0
}
group2 {
atomsFile colvar_ref.pdb
atomsCol B
atomsColValue 3.0
}
}
}
colvar {
name DistInv-PouHD
width 0.5
distanceInv {
exponent 10
group1 {
atomsFile colvar_ref.pdb
atomsCol B
atomsColValue 2.0
}
group2 {
atomsFile colvar_ref.pdb
atomsCol B
atomsColValue 4.0
}
}
}
harmonic {
colvars DistInv-PouS
centers 5
targetCenters 40
targetNumSteps 10000
outputCenters on
outputAccumulatedWork on
forceConstant 10.0
}
-- Vlad Cojocaru, Ph.D., Project Group Leader Department of Cell and Developmental Biology Max Planck Institute for Molecular Biomedicine Röntgenstrasse 20, 48149 Münster, Germany Tel: +49-251-70365-324; Fax: +49-251-70365-399 Email: vlad.cojocaru[at]mpi-muenster.mpg.de http://www.mpi-muenster.mpg.de/43241/cojocaru
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