Justin A. Lemkul
jalemkul at vt.edu
Tue Mar 17 15:34:30 CET 2009
Emanuel Peter wrote:
> Dear Gromacs users,
> I have read about an equilibration procedure for proteins.
> It has the following sequence:
> - cool down to 20 K an let this run for about 1 ps.
> - heat the system up with 10 K every 500 steps until you get 300 K.
> - do a run for 4 ps at 300 K.
> Is this kind of equilibration really necessary ?
> At the moment I do not know for what reason one should equilibrate in
> this way.
IMHO, it's unnecessary. Warming up a system slowly is not unreasonable, but
I've always done straight equilibration at the desired temperature and/or
pressure and achieved reasonable results.
> One told me that he removed stepwisely constraints while equilibrating.
> Could anyone tell me why one should equilibrate with this scheme ?
Constraints or restraints? These are separate concepts in Gromacs. Removing
constraints seems pointless, unless you want to start using a smaller timestep!
Slowly removing restraints (like position restraints) might be necessary for a
very sensitive system, but for a standard protein in water, it's probably excessive.
> Thanks in advance.
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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