From: Almeida-Hernández, Yasser, Dr. (yasser.almeida-hernandez_at_uni-due.de)
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?
Best,
Yasser
________________________________
From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
Sent: Monday, December 27, 2021 5:14:57 PM
To: NAMD list; Almeida-Hernández, 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 Å, 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:
https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html*sec:units__;Iw!!DZ3fjg!ui7KrEjvrrh8S5NdFLmRweKzpv7nSplHV0Kz3XSw3lEZPGymuBhTEMo8XGnkNMJ7qQ$
and NAMD uses kcal/mol.
Giacomo
On Mon, Dec 27, 2021 at 5:47 AM Almeida-Hernández, Yasser, Dr. <yasser.almeida-hernandez_at_uni-due.de<mailto:yasser.almeida-hernandez_at_uni-due.de>> 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.
Best,
Yasser
-- Dr. Yasser Almeida-Hernandez Postdoctoral Researcher Computational Biochemistry group T01 R03 D45 Faculty of Biology University of Duisburg-Essen Universitätsstr. 2, 45117 Essen Email: yasser.almeida-hernandez_at_uni-due.de<mailto:%20yasser.almeida-hernandez_at_uni-due.de> Phone: +49 201 183 2457<tel:+49%20201%20183%202457>
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