Re: TMD questions - refined

From: Ashkan Shekaari (
Date: Thu Oct 01 2020 - 09:14:33 CDT

Dear researcher,

TMD is not suitable for ligand binding problems.
Use steered molecular dynamics (SMD).
TMD is specialized to extract conformational transition pathways
and the associated hot sites involved in the transition.

All the best, 
Ashkan Shekaari, 
Ph.D Candidate in Solid State Physics, 
K. N. Toosi University of Technology, 
Tehran, Iran 
From: "Nadia Elghobashi-Meinhardt" <> 
To: "namd-l" <> 
Sent: Thursday, October 1, 2020 5:29:18 PM 
Subject: namd-l: TMD questions - refined 
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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