From: Almeida-HernŠndez, Yasser, Dr. (yasser.almeida-hernandez_at_uni-due.de)
Date: Mon Dec 27 2021 - 04:45:32 CST
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:
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
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 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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