How does NAMD calculate AccumulatedWork when using RMSD colvar?

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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