From: Asghar Razavi (asr2013_at_med.cornell.edu)
Date: Thu Apr 12 2018 - 12:29:19 CDT
Hello,
I am using RMSD colvar module to guide simulation from an outward-facing to inward-facing structure in a membrane protein.
I was wondering how NAMD calculates accumulated work in every step?
This is the output of the colvars.traj:
# step d1 v_d1 fs_d1 fa_d1 E_distance_vector x0_d1 W_distance_vector
120 9.67004669488418e+00 0.00000000000000e+00 0.00000000000000e+00 2.99533051158161e+00 4.48600243680586e-02 9.70000000000000e+00 0.00000000000000e+00
121 9.67003869615287e+00 -3.99936565731451e-06 -4.63815041079987e+01 2.83116439831854e+00 4.00774592515320e-02 9.69835034013605e+00 -4.67045827613773e-03
122 9.66354739186415e+00 -3.24565214436046e-03 -4.26702431934563e+01 3.31532884079611e+00 5.49570266130722e-02 9.69670068027211e+00 -1.01396232005803e-02
123 9.66353581631177e+00 -5.78777618720494e-06 -7.59630239708717e+00 3.15152040963902e+00 4.96604044618565e-02 9.69505102040816e+00 -1.53385599307671e-02
124 9.65053306451860e+00 -6.50137589658772e-03 7.47456654403538e+00 4.28682960256204e+00 9.18845402070110e-02 9.69340136054422e+00 -2.24103706696875e-02
..
6118 5.14921104325620e+00 -9.23623037137666e-04 6.17680155218682e+02 -5.14921104325527e+02 1.32571871839910e+03 9.24720803402446e-13 3.35332266426346e+03
6119 5.14724039052091e+00 -9.85326367642703e-04 4.65634315698935e+02 -5.14724039051999e+02 1.32470418189002e+03 9.24720803402446e-13 3.35417178385169e+03
6120 5.14537025388350e+00 -9.35068318706822e-04 3.28085289472514e+02 -5.14537025388257e+02 1.32374175247698e+03 9.24720803402446e-13 3.35502059493099e+03
I am assuming it should use "displacement" times "force" to calculate work. Where are the "displacement" and "force" is the above log file? I can't mach any to the "W_distance_vector".
This is the input file for RMSD colvar:
colvarsTrajFrequency 1
harmonic {
name distance_vector
colvars d1
forceConstant 100
centers 9.7
targetCenters 0.0
targetNumSteps 6000
outputAccumulatedWork
outputEnergy
outputCenters
}
colvar {
name d1
outputAppliedForce on
outputSystemForce on
outputVelocity on
rmsd {
atoms { psfSegID A A
atomNameResidueRange CA 18-105
atomNameResidueRange CA 130-414
}
refPositionsFile ./ref_ifs_CA_2.pdb
refPositionsCol B
refPositionsColValue 1.00
}
}
Thank you,
Asghar Razavi
-----------------------------------------------
Asghar Razavi
Postdoctoral Associate
Department of Physiology and Biophysics
Weill Cornell Medical College (WCMC)
1300 York Avenue, Room C503
New York, NY 10065<http://maps.google.com/maps?z=16&q=1300+york+avenue,+room+c503+new+york,+ny+10065>
Email: asr2013_at_med.cornell.edu
Website: <http://physiology.med.cornell.edu/faculty/hweinstein/index.html> https://asgharrazavi.net
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