From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
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:
https://github.com/colvars/colvars/blob/master/examples/05_targeted_MD.colvars.in?raw=true
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.
Giacomo
On Mon, Jan 2, 2017 at 11:43 AM, Steven Cohen <secohen_at_mit.edu> 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
> secohen_at_mit.edu
>
-- 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 Scholar: http://goo.gl/Q3TBQU Personal: http://giacomofiorin.github.io/ Lab page: https://icms.cst.temple.edu/members.html *"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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