[gmx-users] Constraining positions according to B-factors

[Tsjerk Wassenaar]

Hi Irem,

Okay. First remove all bonded and nonbonded interactions, because these are
what gives rise to the thermal fluctuations in a real crystal. So you would
only need an [ atoms ] section and a section with [ position_restraints ].
You should be able to calculate a spring constants based on the
experimental b-factors. Then, if you perform the simulation and calculate
the b-factors, you should be able to reproduce what you put in.

But seriously, why would you want that? There is no force in nature that
keeps atoms pinned to some xyz coordinate in space. What you see as thermal
motion is the result of the constraints due to the interactions there are.
Of course, that means in the context the molecule is in. If you want to
simulate b-factors in a crystal, you've gotta simulate a crystal. Using
physics, not using artificial means to try to reproduce what you put in.

Hope it helps,

Tsjerk


On Fri, Jan 15, 2016 at 3:27 PM, Irem Altan <irem.altan at duke.edu> wrote:

> Hi,
>
> Yes, assuming a harmonic potential, I want to be able to constrain atoms
> such that their mean square displacement during the simulation will be
> compatible with their B-factors.
>
> Best,
> Irem
>
> > On Jan 15, 2016, at 1:32 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> >
> > Hey,
> >
> > Under the assumption that the B-factor is caused by some atom-specific
> > force that keeps it pinned to a certain position?
> >
> > Cheers,
> >
> > Tsjerk
> > On Jan 15, 2016 01:18, "Irem Altan" <irem.altan at duke.edu> wrote:
> >
> >> Hi,
> >>
> >> I was wondering if it was possible to constrain protein atom positions
> >> according to their B-factors, so that their RMS displacement during the
> >> simulation will be compatible with their B-factors. If so, could you
> point
> >> me towards a helpful resource?
> >>
> >> Best,
> >> Irem
> >> --
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-- 
Tsjerk A. Wassenaar, Ph.D.