Re: SMD at constant velocity

From: Almeida-HernŠndez, Yasser, Dr. (
Date: Tue Dec 28 2021 - 04:45:00 CST

Dear Giacomo,

Thank you for your reply.

I've tried with different initial and final centers, up to 10 A apart, and the same happens. The proteins reach the targetCenters very fast and stay there, while the centers evolve linearly until the end of the simulation.

What do you think could be the problem?



From: Giacomo Fiorin <>
Sent: Monday, December 27, 2021 5:14:57 PM
To: NAMD list; Almeida-HernŠndez, Yasser, Dr.
Subject: Re: namd-l: SMD at constant velocity

Hi Yasser, it sounds like the variables' values do not evolve as you expect them to, but the restraint centers do work as expected. This is not uncommon.

Your initial and final centers differ by only 0.5 Ň, and assuming you used the default width of 1, for a force constant of 5 kcal/mol you get 1/2◊5◊0.5^2 = 0.625 kcal/mol, roughly one kT unit. Not much difference between those states as far as the restraint is concerned.

Accumulated work, like all energies, is in the same unit of the MD engine that Colvars is distributed with, in this case NAMD:*sec:units__;Iw!!DZ3fjg!ui7KrEjvrrh8S5NdFLmRweKzpv7nSplHV0Kz3XSw3lEZPGymuBhTEMo8XGnkNMJ7qQ$
and NAMD uses kcal/mol.


On Mon, Dec 27, 2021 at 5:47 AM Almeida-HernŠndez, Yasser, Dr. <<>> wrote:

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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