Re: Query regarding colvar distanceZ

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Dec 26 2016 - 08:12:23 CST

Hi Peter,

What are the colvars values at time zero if you do it either way? It should be reported in the (very short) colvars.traj file. It sounds like what are reasonable boundaries and centers for the distance are not reasonable for distanceZ, and so the simulation gets a gigantic force and leads to atoms moving too fast.

Josh Vermaas

Director’s Postdoctoral Fellow
National Renewable Energy Laboratory
joshua.vermaas_at_nrel.gov<mailto:joshua.vermaas_at_nrel.gov>

On Dec 26, 2016, at 5:57 AM, Peter Mawanga <peter.mawanga.lagos_at_gmail.com<mailto:peter.mawanga.lagos_at_gmail.com>> wrote:

Hello everyone

I want to apply colvar distanceZ for my NAMD ABF simulation instead of distance. But each time the simulation keeps crashing (atoms moving too fast) for distanceZ but works perfectly fine with distance colvar. Please check the input file below:

colvarsTrajFrequency 10000
colvarsRestartFrequency 10000

colvar {
name polymerbeadseparation
width 0.1
lowerboundary 5.0
upperboundary 30.0
lowerwallconstant 100.0
upperwallconstant 100.0
  expandBoundaries on

//distance

distance {
group1 {
atomnumbers {17}
}
group2 {
atomnumbers {51}
}
oneSiteTotalForce yes
}

//distanceZ

distanceZ {
main {
atomnumbers {17}
}
ref {
atomnumbers {51}
}
axis (1, 0, 0)
oneSiteTotalForce yes
}

abf {
colvars polymerbeadseparation
fullSamples 1000
hideJacobian yes
historyFreq 10000
}

Please suggest some solution.

Cheers
Peter

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