Re: Running IMD with TMD (domain restraints)

From: Giacomo Fiorin (
Date: Wed Jan 04 2017 - 08:36:46 CST

Hi Steven, you could tweak the TMD feature to set a constant restraint
potential, but this is more cleanly done through Colvars, by setting one
RMSD collective variable and applying a constant harmonic restraint on it.
For multiple domains, simply define a distinct RMSD variable for each.

You can easily adapt the following to remove the time-dependent options:

To drag a domain onto an EM map, you should also consider the
MDFF/gridForces feature. Manual dock is great for demonstrations, but I
presume you'll want you results peer-reviewed eventually.


On Mon, Jan 2, 2017 at 11:43 AM, Steven Cohen <> wrote:

> Hi all,
> I was wondering if it is possible to run IMD with domain restraints, as
> are used in TMD simulations. I have a protein which moves according to a
> hinge mechanism, but my TMD simulations tend to get stuck in a relative
> minimum that we know is not physiologically possible. In short, I want to
> use IMD to drag a domain as a whole into my EM map. Is this possible?
> Best,
> Steve
> --
> Steven Cohen
> Graduate Student, Drennan Lab
> Department of Chemistry
> Massachusetts Institute of Technology

Giacomo Fiorin
Associate Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704D
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213
Lab page:
*"As computer programmers we have a responsibility to make sure that we run
the computers instead of the computers running us."*  - Steve Oualline

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