[gmx-users] Re: v-rescale

[Michael Shirts]

I've done some extensive testing (paper on testing method in the
works) and vrescale gives a very accurate ensemble very well for NVT.
Parrinello-Rahman and MTTK are the only algorithms that are correct
for NPT.  Berendsen barostat is not.  Note that there is a bug with
vrescale + md-vv + that is fixed in 4.6 and (hopefully) for the next
patch of 4.5.

For equilibrating a system, Berendsen for both temperature and
pressure is the best bet.  They artificially minimize fluctuations,
which is great for equilibration, bad for data collection.

On Thu, Sep 20, 2012 at 6:05 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 20/09/2012 9:35 AM, Peter C. Lai wrote:
>>
>> I am not sure where the idea of using berendsen barostat with the
>> v-rescale
>> thermostat for equilibration came from, however. Doesn't the typical
>> equilibration begin with v-rescale for temperature equilibration then
>> adding parinello-rahman barostat then switching to nose-hoover for
>> production
>> runs (as nose-hoover chains result in the correct canonical distribution)?
>
>
> N-H does have known issues, see
> http://link.aip.org/link/doi/10.1063/1.2989802 and
> http://link.aip.org/link/doi/10.1063/1.2408420. I am not aware of any
> shortcomings of the Bussi v-rescale thermostat in GROMACS.
>
> Mark
>
>
>>
>> On 2012-09-19 04:24:27PM -0700, Ladasky wrote:
>>>
>>> Dear Sara,
>>>
>>> I just had a problem with my simulations that I traced to the use of the
>>> V-rescale temperature algorithm.  Here is my recent post:
>>>
>>>
>>> http://gromacs.5086.n6.nabble.com/Re-Water-molecules-cannot-be-settled-why-td4999302.html;cid=1348087067061-71#a5001121
>>>
>>> V-rescale may be appropriate in certain simulations, but it is apparently
>>> NOT appropriate when used with Berendsen pressure coupling during the
>>> initial equilibration.  I don't know if that is related to your problem,
>>> but
>>> it's something that I just discovered the hard way.
>>>
>>>
>>>
>>> --
>>> View this message in context:
>>> http://gromacs.5086.n6.nabble.com/v-rescale-tp5001066p5001122.html
>>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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