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

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Apr 12 2018 - 14:54:13 CDT

I just noticed that you have written the trajectory file at every step: try
computing the work as defined, and let me know if it doesn't sum up
correctly. From the look of it I presume you have a more recent version
than this commit:
https://github.com/Colvars/colvars/commit/52f66e0b7dede1549d3faeb420119fb305ab223e

Giacomo

On Thu, Apr 12, 2018 at 3:49 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> 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
>

-- 
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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