Dear Gromacs Users
I have set my pull option as "constant force" and the pull geometry is
"distance"
the manual has stated that the pull_k1 unit is kJ/mol/nm . does it mean that
the force applied to the
protein is proportional to the distance between the 2 groups ? else what is
it ?
No, kJ/mol is an energy unit, so kJ/mol/nm is a force unit -> the force
does not depend on the distant, but is constant. One important think is
that, if you want your force in pN you must transform this value to
kJ/mol/nm.
my second question is that what is the preferable choice for the pull ref
group (pull_group0) in a protein when the force is exerted to the first and
last res of the molecule .
You want the first / last residue as pull_group0 / pull_group1 (or in
diferent order). If you then take the full residue or only one or a
couple of atoms is up to you.
Greetings
Thomas
Best Regards
Ali
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