[gmx-users] Using nose-Hoover thermostat with berendsen barostat

[jay patil]

Thanks Justin, Mark. 

Yogesh

> On 19-Jul-2017, at 6:42 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
>> On 7/18/17 9:23 AM, jay patil wrote:
>> The reason for using berendsen is: I thought parrinello is sensitive, it's not wise to use it while equilibrating. So I was trying to use berendsen for equilibration and then production run with parrinello.
>> One more thought, my system is not well equilibrated, I know because it got disturbed when I pulled one water molecule from solvent region into the bilayer. Which disrupted the Bilayer a little bit. Then my system should blow up in initial stages only may be because of overlap. Why it is blowing up after few nano seconds of simulation.
> 
> Crashes can occur at any time; they're more frequent right at the outset but bad physics can manifest at any point.  If the system ran fine without any biasing potential, but then you turn on a bias and things become unstable, you should be troubleshooting whatever restraints you've added, not the barostat.  The pressure instability is a symptom, not a cause.
> 
> -Justin
> 
>> Some insights will be helpful.
>> Thanks
>> Yogesh
>>> On 18-Jul-2017, at 5:37 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>>> 
>>> Hi,
>>> 
>>> The more Berendsen you use, the less physics you get ;-)
>>> 
>>> Mark
>>> 
>>>> On Tue, 18 Jul 2017 13:44 jay patil <jpatil911 at gmail.com> wrote:
>>>> 
>>>> Hi Experts,
>>>> Can we use nose-Hoover thermostat in combination with berendsen barostat.
>>>> When I use grompp command, it gives warning berendsen will not give true
>>>> ensemble, and with -maxwarn 1 option I am able to run the simulation.  My
>>>> doubt is: can we use this combination of thermostat and barostat. Or both
>>>> should be berendsen.
>>>> Any suggestion will be helpful.
>>>> 
>>>> Thanks
>>>> 
>>>> Yogesh
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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