[gmx-users] A theoretical question

Javier Cerezo jcb1 at um.es
Tue Feb 28 11:02:11 CET 2012

Hi Jiangfeng

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 
thermodynamic ensemble.


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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PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434

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