From: Jiali Wang (jwang204_at_binghamton.edu)
Date: Wed Jun 10 2020 - 12:54:51 CDT
Dear NAMD users,
Good afternoon, I am using harmonic force to push two atom together, with
set a colvars to tracking the distance from around 50A to 0A. However, even
I set "forceNoPBC on", but the moving atom still jump from center
simulation box to other periodic environments, detail setting as following,
is there something wrong in my file?
I want to track the distance and save into frames to run the potential mean
force calculations.
best,
Jiali
colvarsTrajFrequency 500
colvar {
name length
outputAppliedForce off
distance {
forceNoPBC on
group1 {
atomNumbers 18937
}
group2 {
atomNumbers 91692
}
}
}
harmonic {
name lenpot
colvars length
forceConstant 20 # in kcal/mol/A^2
forceNoPBC yes
centers 56 # go from 25 Angstrom RMSD...
targetCenters 0 # ... to 1 Angstrom
targetNumStages 20 # n-1 steps of calculation
targetNumSteps 20000 #[expr total ${numsteps} / 10
targetnumberstages]
outputCenters on
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2020 - 23:17:13 CST