[gmx-users] Parrinello-Rahman vs. Nose-Hoover
nedomacho at gmail.com
Wed May 29 05:29:14 CEST 2019
Different simulators use different thermostats and barostats, and given
that molecular simulations are a lot like grandma's cooking, there is no
truly clear answer to your question. However, I do have a few
suggestions. If you want to recreate exactly what your colleague did,
use LAMMPS -- its a neat software package. What barostats and
thermostats to use, and it what combination, should not come from a
colleague, but is supposed to be a judicious choice, based on a
reasonable understanding of the math behind these methods.
Side note: In my opinion, Gromacs did everyone a huge favor not
implementing the pure piston-type Nose-Hoover barostat. If it were up to
me, given how much insane oscillatory garbage these algorithms (in
combination with users who treat simulation software as a black box)
produce in the literature, I would remove Nose-Hoover style control
algorithms permanently from all simulators forever -- except for maybe
incredibly well-behaved pre-relaxed ensembles larger than 100K atoms.
On 5/28/2019 9:08 PM, Anh Vo wrote:
> Previously, as my colleague performed the same simulation with me (POPC
> bilayer membrane under equibiaxial tension) in LAMMPS, he could use
> Nose-Hoover for both temperature and pressure coupling. But in GROMACS when
> I tried to re-do what he has done, I could not use Nose-Hoover for pressure
> coupling. GROMACS just allows me to choose among Berendsen,
> Parrinello-Rahman, Isotropic or MTTK options. And in the manual it is said
> that "In most cases Parrinello-Rahman barostat would be combined with the
> Nose-Hoover thermostat as the most practical choice". Hence, I don't know
> why that is the most practical choice?
> And *why is Nose-Hoover not used for pressure coupling in GROMACS as it is
> used in LAMMPS?*
> Thank you a lot.
> Anh Vo
>> -----Original Message-----
>> Message: 3
>> Date: Wed, 29 May 2019 00:51:41 +0200
>> From: Mark Abraham <mark.j.abraham at gmail.com>
>> Why should it be used? :-)
>> On Tue, 28 May 2019 at 23:28, Anh Vo <atv55 at msstate.edu> wrote:
>>> Hi all,
>>> In GROMACS Manual, it is said that "In most cases Parrinello-Rahman
>>> barostat would be combined with the Nose-Hoover thermostat as the most
>>> practical choice", and I see that Nose-Hoover algorithm is only
>>> available for temperature coupling, not pressure coupling. Why is
>>> Nose-Hoover not used for pressure coupling in GROMACS?
>>> Thank you very much.
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