[gmx-users] Re: Nose-Hover chains for membrane protein simulation

[James Starlight]

Michael,


thanks for suggestions.

the main reason of ussage N-H with chains is the assumption that simple N-H
does not provide ergodicity of the system assuming that I'd like to sample
all temperature acceptable conformations on the 100 ns trajectory.

But as I understood the chain regime does not compatible with the membrane
protein simulation due to the artifacts arising with MTTK batostat.

James

2013/6/1 Michael Shirts <mrshirts at gmail.com>

> I can't think of any instance where nose-hoover chains provides an
> advantage over nose-hoover in a large system -- all the demonstrations
> of superiority are in model systems that are not particularly chaotic.
>  As the system gets more chaotic, it matters less.
>
> I would go with md, nose-hoover (w/o chains), and Parrinello-Rahman
> with semiisotropic scaling.
>
> On Sat, Jun 1, 2013 at 1:07 AM, James Starlight <jmsstarlight at gmail.com>
> wrote:
> > Performing 5ns simulation after 2 ns equilibration in NPT ensemble (MTTK
> > barostat 5ps coupling ) I've observed non-physical behaviour of my system
> > with the constant drift of the protein molecule as the rigid body in the
> > y-z plane
> >
> > Energy                      Average   Err.Est.       RMSD  Tot-Drift
> >
> -------------------------------------------------------------------------------
> > Pressure                   -760.137         --    193.776    218.059
>  (bar)
> >
> >
> > >From manual I've noticed that MMTK doest not support *semiisotropic
> > scalling.  *Doest it means that with the Nose-hover chains and md-vv I
> > should use only weaker coupling during productions runs (I cant use
> > Parinello;s barostat with such options too)
> >
> > Thanks for help
> >
> > James
> >
> >
> >
> > 2013/5/31 James Starlight <jmsstarlight at gmail.com>
> >
> >> Dear Gromacs users!
> >>
> >> I'd like to perform simulation of the membrane protein in lipid-water
> >> system using Nose-Hover with chains.
> >>
> >> From manual I've found that with such thermostat I should use (1) md-vv
> >> integrator (2) MTTK  instead of Parinello's batostat  and (3) shake
> instead
> >> of LINCS.
> >>
> >>
> >> How doest such options compatible with the simulation of membrane
> proteins
> >> in general ? On what other options should I pay attention during
> simulation
> >> of membrane protein with NH chains ?
> >>
> >>
> >>
> >> Thanks for help,
> >> James
> >>
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