[gmx-users] Parrinello-Rahman vs. Nose-Hoover

[Alex]

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.

Alex

On 5/28/2019 9:08 PM, Anh Vo wrote:
> Hi,
>
> 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.
>
> Best,
> Anh Vo
>
>
>>   -----Original Message-----
>>
>>
>> Message: 3
>>
>> Date: Wed, 29 May 2019 00:51:41 +0200
>>
>> From: Mark Abraham <mark.j.abraham at gmail.com>
>>
>>
>>
>> Hi,
>>
>>
>>
>> Why should it be used? :-)
>>
>>
>>
>> Mark
>>
>>
>>
>> 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.