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

Michael Shirts mrshirts at gmail.com
Sat Jun 1 18:01:12 CEST 2013

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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