[gmx-users] Re: v-rescale

[Mark Abraham]

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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