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 Mar 12 2020 - 11:30:02 PDT
