From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Dec 14 2015 - 10:55:36 CST
Hello Bryan, the output is in the column labeled as "W_<variable name>".
Does the last number in that column correspond to what you have in the
state file?
Giacomo
On Sun, Dec 13, 2015 at 8:36 PM, Bryan Roessler <roessler_at_uab.edu> wrote:
> 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>*
> Knowledge that will change your world
>
>
-- Giacomo Fiorin Assistant Professor of Research Institute for Computational Molecular Science (ICMS) College of Science and Technology, Temple University 1925 North 12th Street (035-07), Room 704D Philadelphia, PA 19122-1801 Phone: +1-215-204-4213 http://goo.gl/Q3TBQU http://giacomofiorin.github.io/ https://icms.cst.temple.edu/members.html
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