[gmx-users] heating

[Dmitry Kovalsky]

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
> conformations.

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)?

-- 
Sincerely yours,

Dima

Ph.D. Student Dmitry Kovalsky
Institute of Molecular Biology & Genetics
150 Akad. Zabolotnogo Street,
Kiev-143, 03143
UKRAINE

E-mail: dikov at imbg.org.ua
Fax:  +380 (44) 266-0759
Tel.: +380 (44) 266-5589