A short update on this topic for the record in case anyone tries to
answer a similar question ...
In my initial trial simulations with ff19SB + OPC water model l observe
the same collapse of the 2 domains of this DNA binding protein as
observed with ff14SB+SPC/E (qualitatively) ...
I do not have any experimental data on whether this collapse is part of
the real dynamics of the protein but my intuition says that such a
collapse even if it exists it should be very short lived because these
domains bind to DNA independently ...
Anyhow, these results are preliminary and only qualitative , the
simulations are still short (500 ns) but still once collapsed (fairly
fast), the domains do not move away from each other. Therefore, I have
the feeling that the combination ff19SB+OPC water model still leads to
overly compact states in such cases ....
Best
Vlad
On 2020-03-12 19:03, Vlad Cojocaru wrote:
> Would you recommend ff19SB + OPC water model for such a system ?
>
> On 3/12/20 2:58 PM, Carlos Simmerling wrote:
>> I would look into the water model. Many of the older models have a
>> too-weak
>> dispersion interaction with the solute, and lead to overly compact
>> states.
>> This is documented in IDP and unfolded protein simulations, and also
>> discussed in our ff19SB paper.
>>
>> On Thu, Mar 12, 2020, 5:58 AM Vlad Cojocaru <
>> vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>>
>>> Dear all,
>>>
>>> We are doing some explicit solvent simulations (ff14SB, SPC water
>>> model,
>>> PBC, 250 ns till now) of different modular proteins that have 2 domains
>>> connected by a flexible linker of 17 to 31 aminoacids. We are
>>> interested
>>> in the structural ensemble adopted by the linker region in the presence
>>> of the 2 domains and how it influences the relative motion of the
>>> domains.
>>>
>>> However, in all simulations the domains colapse on each other quite
>>> fast
>>> and get stuck, not much inter domain motion happening after the
>>> colapse.
>>>
>>> Does any of you have experience with such systems and if yes, could you
>>> share this experience ? Is this behavior we observe expected ? Is it
>>> dependent on the force field , water model or other parameters ?
>>>
>>> Thanks for any advice
>>>
>>> Best wishes
>>> Vlad
>>>
>>>
>>>
>>>
>>>
>>> --
>>> Vlad Cojocaru, PD (Habil.), Ph.D.
>>> -----------------------------------------------
>>> Project Group Leader
>>> Department of Cell and Developmental Biology
>>> Max Planck Institute for Molecular Biomedicine
>>> Röntgenstrasse 20, 48149 Münster, Germany
>>> -----------------------------------------------
>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>>>
>>>
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--
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Thu Apr 16 2020 - 03:00:02 PDT
