[gmx-users] Equilibration

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.
> Emanuel
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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