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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Received on Thu Mar 12 2020 - 07:00:01 PDT
