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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Received on Wed Jul 23 2014 - 08:30:02 PDT
