SMD at constant velocity

From: Almeida-HernŠndez, Yasser, Dr. (
Date: Mon Dec 27 2021 - 04:45:32 CST

Dear all,

I am struggling with a SMD at constant velocity, where I want to pull two proteins continuously along the X-axis apart, at k = 5 kcal/mol at 0.5 A/ns, during 50 ns

Below is the definition of the harmonic:

harmonic {
   colvars pull_nter pull_cter pull_nter_y pull_cter_y pull_nter_z pull_cter_z
   centers -20.0 20.0 0.0 0.0 0.0 0.0
   targetCenters -20.5 20.5 0.0 0.0 0.0 0.0
   forceConstant 5.
   targetNumSteps 25000000
   outputCenters yes
   outputAccumulatedWork yes

I have tried several centers and targetCenters to achieve the velocity, but what happens is that the targetCenters are reached very fast and then the proteins stay there. However, I write the centers during the simulation (with outputCenters, x0_pull_nter and x0_pull_nter) and they change continuously as expected until the end of the run.

Am I missing something?

Also, what are the units of the accumulated work written in the .traj file?

Any help will be very much appreciated.



Dr. Yasser Almeida-Hernandez
Postdoctoral Researcher
Computational Biochemistry group
T01 R03 D45
Faculty of Biology
University of Duisburg-Essen
Universitštsstr. 2, 45117 Essen
Phone: +49 201 183 2457<tel:+49%20201%20183%202457>

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