[gmx-users] Differences between Parrinello-Rahman, Nose-Hoover and MTTK - between LINCS and SHAKE

[Mark Abraham]

Hi,

On Mon, 20 May 2019 at 19:55, Anh Vo <atv55 at msstate.edu> wrote:

> Hi All,
>
> I’m currently running GROMACS to simulate a simple phospholipid bilayer
> membrane (POPC) under deformation.
>
> 1. For production step, GROMACS does not allow me to use Nose-Hoover
> barostat for pressure coupling, I can only choose among Berendsen,
> Parrinello-Rahman, Isotropic or MTTK options.
>
> What are the differences between *Parrinello-Rahman, Nose-Hoover and MTTK?*
>

There's some good background information at
http://manual.gromacs.org/current/reference-manual/algorithms/molecular-dynamics.html#pressure-coupling.
Berendsen does not sample a relevant distribution. N-H has doubtful ability
to sample ergodically, but probably is the best practical choice. MTTK
perhaps has some theoretical advantages, but cannot be used with
constraints, so the loss in sampling / increased cost is probably
ineffective overall.

Nose-Hoover can be used for temperature coupling, but not for pressure
> coupling. Why is that?
>

P-R barostat has never been implemented.


> 2. I'm not very clear what is constraints?


Constrained bonds cannot oscillate. The fastest oscillations in the system
restrict the size of the timestep that can be taken, those are the bond
vibrations involving H atoms. It has been found that rigid bonds are
roughly good a model as simple Hookes springs, and permit a larger
timestep. The larger timestep permits better sampling.

And what are the differences
> between LINCS and SHAKE constraint algorithm?
>

Very little, but LINCS is the algorithm of choice in GROMACS because it can
be parallelised well.
http://manual.gromacs.org/current/reference-manual/algorithms/constraint-algorithms.html

3. What does "refcoord_scaling" do in pressure coupling?
>

Scales the reference coordinates for position restraints - do check out the
mdp option documentation :-)

Mark

Thank you very much for sharing your time.
>
> Best regards,
> Anh Vo
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