I don't think any degree of boost will overcome suitably defined cartesian
restraints, although something tells me mixing those two together could
cause some instabilities in the integration (just a hunch though).
If I recall, the boost estimates require the number of degrees of freedom
as an input. You might consider calculating the boost by excluding the
restrained atoms (*i.e.* treat them as constraints).
Regards,
Brian
On Wed, Jul 23, 2014 at 10:54 AM, 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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--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for
Integrative Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
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08854-8066
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Received on Wed Jul 23 2014 - 09:00:02 PDT
