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

[Irem Altan]

Hi,

Thank you for your answer, I will try that. I realize it’s unphysical, but I want to compare certain properties of the protein to diffraction data.
Just to double check: the values in [position_restraints] are in units of kJ/(mol*nm^2), right?

Best,
Irem

> On Jan 15, 2016, at 9:47 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 
> 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.
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