[gmx-users] RE: A theoretical question

[Mark Abraham]

On 28/02/12, "Kukol, Andreas" <a.kukol at herts.ac.uk> wrote:

> Hello,
> 
> Firstly, proper equilibration is a technical requirement. The production MD simulation might crash, if the system was not properly equilibrated.
> 
> Secondly, if you want to study the properties of a macromolecule in solvent, you must do a macromolecule position-restraint equilibration. Otherwise, the structure of the macromolecule would be distorted in a non-natural way.

 
... assuming that the initial structure is representative of the true ensemble and that the equilibration might be so rough as to distort that, and that you wish to follow the dynamics from that particular starting point for some reason.
 
Mark 
 

> 
> 
> 
> Best wishes
> Andreas
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] <gmx-users-bounces at gromacs.org]> On Behalf Of Du Jiangfeng (BIOCH)
> Sent: 28 February 2012 09:46
> To: gmx-users at gromacs.org
> Subject: [gmx-users] A theoretical question
> 
> 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
>     Mobile: +31-681741859
>     FAX: +31-43-3884159
>     6200 MD Maastricht
>     The Netherlands-- 
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