dikov at imbg.org.ua
Thu Oct 17 12:49:03 CEST 2002
On Thursday 17 October 2002 10:17, gmx-users-request at gromacs.org wrote:
> > Hi,
> > I'm wonedring about of use of heating procedure while preparing the
> > system for simulation.
> > I mean what kind of errors and advantages it can introduce into the
> > system to be simulated?
> I usually don't do it.
> Advantage: you could probe regions of phase-space that are otherwise
> unavailable. I.e. you can find a lower energy minimum, or a more stable
> state, or an interesting other feature.
> Disadvantage: you could end up in regions of phase-space that are otherwise
> unavailable. I.e. you can get 'trapped' in unrealistic or irrelevant
Thanks for a reply
What is the most tolerant method to perform short system eqilibibration MD
after postion restraints and before data collection MD? I mean is it
efficient to perform simple MD for a e.g. 500 psec or MD with stepwise
decrease of position restraint term (or similar)?
Ph.D. Student Dmitry Kovalsky
Institute of Molecular Biology & Genetics
150 Akad. Zabolotnogo Street,
E-mail: dikov at imbg.org.ua
Fax: +380 (44) 266-0759
Tel.: +380 (44) 266-5589
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