Could you please tell me if the constraint forces are included in the
forces outputed in the trr file?
Constraint forces are not included. We should state this somewhere in the
manual.
I wondered about this before as well. Shouldn't we include them anyway?
It is quite important when you use the forces for e.g. computing a
You don't want to compute PMF from the forces in the trr file.
You need a lot of sampling for a PMF and the trr would become far too big.
Currently we have the pull code and free energy code, both with
umbrella sampling and constraints for determining PMF's.
I prefer to have F=-grad V in the trr file and not the constraint forces.
Thank you very much for all your helps.
That's great! The force without the constraint force is just what I want.
For free energy calculation, I will use thermodynamics intergration or pull
code. Thank you for your kind suggestion.
I wondered about this before as well. Shouldn't we include them anyway?
It might be a good idea to add an option to determine if writing the
constraint force into trr file or not. How do you think?
-- Pu
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