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Biomolecular simulation trajectory/data analysis.
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unit of force in Jarcynski ASMD output #1038

Closed macardosa closed 1 year ago

macardosa commented 1 year ago

Dear Amber team,

I have been trying to figure out what are the units of force printed in the DUMPAVE file from an adaptive SMD simulation as quoted here and in the manual Amber23 page 545. I have the impression they should be kcal/mol/Ang, but since I have not found it explicitly said I wanted to be sure of that. Also, I went to so many emails in the amber mailing list asking about units of force in other contexts, and saying it might be amu Ang/ps^2, that I got a little confused. Finally, I found this other issue which says the units are kcal/mol/Ang in the NetCDF output.

So, please which are the units of force printed in the output file of ASMD: the file with four columns: x0(t), x, force, work.

Kind regards Manuel

drroe commented 1 year ago

Hi! This repository is really just for cpptraj issues - you'll almost certainly get a better response on the Amber mailing list. I'll do my best to respond here.

So, please which are the units of force printed in the output file of ASMD: the file with four columns: x0(t), x, force, work.

I'm not an expert in SMD simulations, but I do know that internally Amber uses AKMA units, so force is going to be kcal/mol/Ang unless there is some conversion going on. But to be certain I would ping the mailing list.

macardosa commented 1 year ago

Thank you to @drroe for addressing so quickly my question. I also found in one of the threads of the Amber mailing list that the units should be kcal/mol/Ang http://archive.ambermd.org/200906/0424.html http://archive.ambermd.org/200611/0143.html

I appreciate your response and I will ask on the Amber mailing list other issues of this kind.