Re: How does NAMD calculate AccumulatedWork when using RMSD colvar?

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Apr 12 2018 - 14:49:04 CDT

HI Asghar, the work is computed as the integral of the force applied by the
harmonic restraint (which equals fa_d1, if there are no other biases) times
the displacement of the restraint center (difference of x0_d1 between
*consecutive* steps, i.e. more often than in the colvars.traj file). For a
distance or distanceZ variable, this is pretty much constant-velocity SMD.

Please note that RMSD = 0 is a singularity for the respective PMF. It may
be better to aim for a final RMSD that equals the magnitude of the thermal
fluctuations.

Giacomo

On Thu, Apr 12, 2018 at 1:29 PM, Asghar Razavi <asr2013_at_med.cornell.edu>
wrote:

> 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
> <https://maps.google.com/?q=CA+18-105&entry=gmail&source=g>
>
> atomNameResidueRange CA 130-414
> <https://maps.google.com/?q=CA+130-414&entry=gmail&source=g>
>
> }
>
> 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
> <https://maps.google.com/?q=1300+York+Avenue,+Room+C503+%0D%0A+New+York,+NY+10065&entry=gmail&source=g>
>
>
> New York, NY 10065
> <https://maps.google.com/?q=1300+York+Avenue,+Room+C503+%0D%0A+New+York,+NY+10065&entry=gmail&source=g>
> <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
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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