From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Tue Sep 09 2014 - 20:31:06 CDT
Hi all,
I'm currently running what's effectively a TMD simulation based on the colvars file pasted in below. Briefly, I have two domains which were previously steered to within ~30 angstroms between their centres of mass, and are now allowed to rattle around within a wall at 31 angstroms. That initial steering simulation ran well (and fast) even with the inclusion of four individual RMSD colvars with harmonic restraints maintaining the internal fold of individual domains.
In the current phase, I'm steering two other groups of atoms - one of which I'm maintaining to the geometry it "found" during the previous phase of the simulation, while the other is steered to a matching configuration over 20ns. There's nothing fundamentally different about this simulation from what I've done to date, yet it's consistently running ~8-fold slower. Just wondering what might be causing this? The only real differences I see are the number of atoms in each colvar (~1500 in this case vs ~50 previously - I'm steering all heavy atoms this time around, rather than just restraining CAs), and the fact that while the individual atoms in each of the current colvars I'm steering are fairly close in 3D space, they're up to a few thousand residues apart in the sequence.
Is this slowdown likely to be a consequence of my setup, or should I look more closely at the cluster? The managers of it assure me there's nothing currently going wrong there...
Thanks,
Tristan
colvarsTrajFrequency 1000
colvarsRestartFrequency 1000
colvar {
name Fn_distance
outputAppliedForce on
upperWall 31.0
upperWallConstant 10
distance {
group1 {
atomsfile colvars.pdb
atomsCol O
atomsColValue 1.0
}
group2 {
atomsfile colvars.pdb
atomsCol O
atomsColValue 2.0
}
forceNoPBC yes
}
}
colvar {
name RMSD_ID_E
rmsd {
atoms {
atomsfile target_ID_sym.pdb # Select biased atoms from this file
atomsCol B # based on beta
atomsColValue 1.0
}
refPositionsFile target_ID_sym.pdb # ref. positions are selected based on atom number
}
}
harmonic {
name ID_E_restrain
colvars RMSD_ID_E
centers 0
targetCenters 0
targetNumSteps 25000000
forceConstant 10
}
colvar {
name RMSD_ID_F
rmsd {
atoms {
atomsfile target_ID_sym.pdb # Select biased atoms from this file
atomsCol B # based on beta
atomsColValue 2.0
}
refPositionsFile target_ID_sym.pdb # ref. positions are selected based on atom number
}
}
harmonic {
name ID_F_steer
colvars RMSD_ID_F
centers 4.8
targetCenters 0
targetNumSteps 10000000
forceConstant 10
}
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