[gmx-users] RE: A theoretical question

Kukol, Andreas a.kukol at herts.ac.uk
Tue Feb 28 11:00:53 CET 2012


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.

Best wishes

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto: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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