From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Jan 14 2020 - 03:44:06 CST

 Hello: is that allowed using a mixture (for different groups of atoms) of
harmonic restraints (by creating a pdb file marked with different values on
column B) and distance colvars?
Could that be equivalent to, or be more appropriate than by, using a
mixture of distance and rmsd colvars for the same different groups of atoms?

The question is related to getting a MD stable system by keeping an
organic ligand at its binding pocket in a model that results from cutting
the natural huge biomolecule all around the ligand.

So far (despite parameterization of the ligand at the state of the art with
CGenFF, whereby it proved stable in TIP3P for hundreds of ns) I was unable
to get a stable system when removing all restraints/colvars except at the
region where the biopolymer was cut..

thanks for a general advice

francesco pietra

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