From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Jul 17 2017 - 13:15:14 CDT
Hi James, typical protocols to do steered MD on a protein (where the list
of atoms involved doesn't change) involve the old SMD code, tclForces or
Colvars.
Again, I would double check the literature about this point. Lipid
molecules fully relax only on a timescale of tens of ns. If you want to
get thermodynamic quantities, you will probably need more 100 ns.
Giacomo
On Mon, Jul 17, 2017 at 12:04 PM, James Starlight <jmsstarlight_at_gmail.com>
wrote:
> Hi Giacomo,
>
> Thanks for the help!
> In a literature I found that 100 ns mechanistic stress is sufficient
> to monitor biologically-active transitions. What NAMD plugins should
> be used for such simulations e.g steered MD or something more special?
>
> Gleb
>
> 2017-07-17 14:49 GMT+02:00 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>:
> > Yes to both, you can control the PBCs (to set e.g. the area strain) and
> > apply restraints or biasing potentials to the protein, but you need to
> > consider carefully the time scale of this process.
> >
> > Giacomo
> >
> > On Mon, Jul 17, 2017 at 3:55 AM, James Starlight <jmsstarlight_at_gmail.com
> >
> > wrote:
> >>
> >> Dear NAMD Users!
> >>
> >> I am using a molecular dynamics simulation for the investigation of
> >> the activation of Mechanic-sensing ionic channel. My question: is it
> >> possible to introduce a mechanical stress acting on the membrane or
> >> directly on selected part of the protein, assuming that its
> >> mechanic-sensing domains are known from the X-ray structure?
> >>
> >> Thanks for help!
> >>
> >> Gleb
> >>
> >
> >
> >
> > --
> > Giacomo Fiorin
> > Associate Professor of Research, Temple University, Philadelphia, PA
> > Contractor, National Institutes of Health, Bethesda, MD
> > http://goo.gl/Q3TBQU
> > https://github.com/giacomofiorin
>
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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