Did you apply restraints to the lipids too? If not then the membrane
bilayer will be destroyed with a higher dihedral boost.
On 23 July 2014 17:54, James Starlight <jmsstarlight.gmail.com> wrote:
> Dan,
>
> so might it be assumed that *biggest* part of the boost will be damped by
> the restraint forces applied on the bigger part of the protein? In this
> case I guess to sample loops only (which are ~1/10 part of my whole system
> for instance) I need to use boost 10 times higher doesn't it?
>
>
> James
>
>
> 2014-07-23 18:02 GMT+04:00 Daniel Roe <daniel.r.roe.gmail.com>:
>
> > On Wed, Jul 23, 2014 at 3:08 AM, James Starlight <jmsstarlight.gmail.com
> >
> > wrote:
> >
> > > I wounder if the dihe boost of this value
> > > have been applied to the whole protein (including its restrained parts)
> > or
> > > only to its unrestrained (in my case loops) parts?
> >
> >
> > Currently the dihedral boost is always applied to all dihedrals. There is
> > no way yet to apply aMD boost to only a subset of dihedrals.
> >
> > -Dan
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 201
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
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--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Wed Jul 23 2014 - 08:30:03 PDT
