[gmx-users] Position restrain in umbrella sampling
rose.rhmn93 at gmail.com
Wed Jun 6 18:12:37 CEST 2018
I checked it for each window. it just oscillates just for 0.1nm in each
window and results are ok.
I just asked to realize your main purpose ...
And i'm convinced now ;) .
Thank you for your kindly and detailed answers like always.
On Wed, 6 Jun 2018, 20:01 Justin Lemkul, <jalemkul at vt.edu> wrote:
> On 6/6/18 11:18 AM, rose rahmani wrote:
> > Hi,
> > I'm doing umbrella sampling for different distances of amino acid from
> > surface.
> > I know that dear Justin warns people that position restraint was for that
> > specific situation in the article mentioned in tutorial and ....
> > I know it doesn't make a sense in my system too in PULLING. But i don't
> > understand why it's not usable for the rest; i mean in nvt_umbrella for
> > each window and conformation. I extract different conformations to show
> > potential of mean force on that exact distance. So if i don't use
> > restraint for AA in for example 0.5nm distance from surface so i can't
> > claim that this nvt_umbrella run is showing the system manner in a
> > situation that AA is about 0.5 from surface because without position
> > restraint(for AA) the AA can be anywhere in box ... . ( i should mention
> > that surface is frozen in my system)Would you please correct me if i'm
> > wrong?
> You shouldn't be layering biases upon biases to try to force a certain
> behavior. It is possible to combine various restraints as long as the
> resulting PMF is corrected for these effects.
> For each window, you define an origin of the umbrella potential. If
> that's 0.5 nm and the specified COM distance (or whatever) does not
> oscillate about this value, then there are two possibilities: (1) Your
> force constant is not large enough or (2) the physical forces in your
> system are such that it is not physically reasonable for the entities to
> exist at that interaction distance.
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
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