[gmx-users] A theoretical question
jcb1 at um.es
Tue Feb 28 11:02:11 CET 2012
Here you have my view on that topic:
You will alway have some equilibration time from a minimized structure,
no mater if you make it on a separate run or not. I mean, the system
will need some time to reach equilibrium conditions, and in case you
don't set separate runs for equilibration you will need to discard the
beginning of your production run until equilibrium is reached (you can
check energy, temperature, pressure...).
The point of making it in different steps is that you can play with the
conditions to make the equilibration process more efficient. For
example, a first NVT equilibration will (quickly) lead you to the target
temperature. Then an NpT equilibration will set the correct pressure. In
both equilibration steps you can use the Berendsen thermostat and
barostat with will efficiently drive your system to your selected
conditions. For production you can then switch to Nose-Hoover and
Parrinelo-Rahman if you are interested in getting a well defined
El 28/02/12 10:45, Du Jiangfeng (BIOCH) escribió:
> Dear GMX-users,
> In my impression, a conventional simulation should be composed by: assemble system --> energy minimization --> NVT and NPT equilibration --> MD simulation, right? Now assume this procedure is correct, how about if there is no equilibration, as long as we set the temperature and pressure at the purposed numbers in MD parameter files?
> Actually, this is puzzling me always.
> Any reply is appreciated.
> Jiangfeng Du, PhD Student
> Cardiovascular Research Institute Maastricht
> Department of Biochemistry
> P.O. Box 616
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Javier CEREZO BASTIDA
Universidad de Murcia
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