From: Bryan Roessler (roessler_at_uab.edu)
Date: Sun Dec 13 2015 - 19:36:26 CST
Hello,
I am performing an RMSD TMD using the colvar module. I have enabled
outputaccumulatedwork, defined colvarsTrajFrequency in my colvars.conf
file, and set a targetCenters as 0.
#colvars.conf
colvarsTrajFrequency 100
colvar {
name RMSD
outputAppliedForce on # keep track of bias force on this variable
rmsd {
atoms {
atomsfile target.pdb # Select biased atoms from this file
atomsCol O # based on occupancy (all nonzero values)
}
refPositionsFile target.pdb # ref. positions are selected based on
atom number
}
}
harmonic { # Define a moving harmonic restraint
colvars RMSD
centers 8.108955 # go from x Angstrom RMSD...
targetCenters 0.0 # ... to 0 Angstrom
targetNumSteps 5000000 # in 5 million MD steps
forceConstant 200. # in kcal/mol/A^2
outputAccumulatedWork yes # keep track of how much energy will be added
}
In my colvars.traj file, I get the following result:
# step RMSD fa_RMSD
W_harmonic1
0 8.10893758151549e+00 3.48369690286177e-03
-5.64982828378909e-09
100 8.11052619012773e+00 -3.46673845550072e-01
5.65938731303684e-05
200 8.11502663013762e+00 -1.27919766752989e+00
1.31113744891078e-04
300 8.11885738603493e+00 -2.07778466699651e+00
3.83688077215023e-04
400 8.12532180221536e+00 -3.40310372308537e+00
8.18258935522487e-04
500 8.12519728600043e+00 -3.41063630010119e+00
1.44251410460275e-03
600 8.10888978266427e+00 -1.81571452874252e-01
1.78822263431076e-03
700 8.10725589897312e+00 1.12769465353679e-01
1.71416299364519e-03
800 8.11735001417091e+00 -1.93848939420818e+00
2.02673879603268e-03
900 8.11555019832383e+00 -1.61096204479421e+00
2.34953782273829e-03
1000 8.11527862312204e+00 -1.58908282444123e+00
2.65996804746196e-03
1100 8.11598268331998e+00 -1.76233068403207e+00
2.98824694512575e-03
1200 8.11313380101662e+00 -1.22499004336234e+00
3.29052949104976e-03
1300 8.10521083280471e+00 3.27167779015269e-01
3.28998207179514e-03
1400 8.12048965688006e+00 -2.76103285605771e+00
3.37644752668391e-03
1500 8.11309309302196e+00 -1.31415590443957e+00
3.70217004390935e-03
1600 8.11441076220149e+00 -1.61012556035054e+00
3.90344676028449e-03
1700 8.11531243386224e+00 -1.82289571250216e+00
4.13469721710158e-03
1800 8.10407381960276e+00 3.92391319390129e-01
4.30633172564267e-03
1900 8.10543201783556e+00 8.83158528271366e-02
4.25614003062294e-03
etc.
and in traj.state:
configuration {
step 5000000
dt 2.000000e+00
}
colvar {
name RMSD
x 2.25972252769051e+00
}
restraint {
configuration {
name harmonic1
centers -5.85060571139554e-10
centers_raw -5.85060571139554e-10
accumulatedWork 1.21825523336397e+03
}
}
So obviously the accumulated work is being calculated, but only output when
the .state file is written (final step), unless I'm missing it elsewhere.
Thanks,
Bryan
*Bryan Roessler | Graduate Research Assistant*
UAB | The University of Alabama at Birmingham
*uab.edu/cmdb <http://uab.edu/cmdb>*
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