TMD questions - refined

From: Nadia Elghobashi-Meinhardt (
Date: Thu Oct 01 2020 - 08:59:18 CDT

Dear NAMD experts,

I am refining the questions I posted recently in the
hope that a TMD expert out there will respond with
some guidance.

I am trying to use TMD to steer a ligand (28 atoms) in a protein (1260
atoms) -
equilibrated system - to a binding pocket that is 15Angstrom away from the
ligand's initial position. Are the following setup steps reasonable?

1) Only protein Calpha atoms and ligand heavy atoms in target position are
in target.pdb
2) The protein is assigned to domain 1 and ligand to domain 2 in
   the beta column
3) The *protein is fitted but not biased in domain1*
4) The *ligand is fitted and biased in domain2*
5) TMDk is 200 in the configuration file
The problem I am having is the following:
over the course of 5ns simulation, barely
any movement of ligand in the direction of target coordinates is observed.

A more general question: Is TMD appropriate for the investigation of ligand
binding or would a colvar_rmsd approach be more suitable?
Any suggestions or tips are a great help!
Thank you in advance.

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