On 28/02/12, "Kukol, Andreas" <[email protected]> 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: [email protected] [mailto:[email protected]] > <[email protected]]> On Behalf Of Du Jiangfeng (BIOCH) > Sent: 28 February 2012 09:46 > To: [email protected] > 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-- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >
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