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.
--
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