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

[Michael Shirts]

And I my point was I didn't think that there was going to be a
measurable ergodicity difference between NH chains and NH.  Given the
size of the system, the chaoticness of atomic motions will likely give
you configurational sampling indistinguishable from full ergodicity.
Most of the errors that are solved by NH chains are for small toy
systems.

On Sun, Jun 2, 2013 at 2:17 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> 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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