[gmx-users] A theoretical question

[Mark Abraham]

On 28/02/12, "Du Jiangfeng (BIOCH)" <j.du at maastrichtuniversity.nl> wrote:

> 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? 

 
If you do that, then the first chunk of your simulation will need to be discarded as part of an equilibration regime. Probably you should do that anyway, even if you have a section you *call* equilibration.
 
However, the real reason for having a separate equilibration part is that various algorithms and parameters are unsuitable for use in a non-equilibrated system. You want to change these later on to those more suitable for long-term use, so you should plan for that in advance. 
 
Mark 
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