[gmx-users] How to make sure to reach the equalibrium state for the protein solution

[Tanping Li]

--- David <spoel at xray.bmc.uu.se> wrote:

> On Fri, 2005-07-29 at 14:50 -0700, Tanping Li wrote:
> > Dear David and all,
> > 
> > I have several questions when I solvate a protein
> in
> > water:
> > 
> > 1. I follow the steps in manual: EM, restrain
> protein
> > MD and full MD. In this process, the Tem is
> increased
> > from intial 30K to final 300K. But I find that the
> > total potential also increases when Tem increase
> to
> > 300K. Does this make sense?
> yes.
> 
> > 
> > 2. I just follow the steps in manual, but I am not
> > sure if I reach to the real equilibrium state
> finally.
> > How to check it? This is the most important thing
> for
> > me now.
> energy and other properties, e.g. RMSD, should
> converge to an
> "equilibrium" value

But How can I know what is the reasonable value for
the "equilibrium" state. Sometimes, protein will be
trapped in a local minimum, and its potential seems to
be "converaged".

> 
> > 
> > 3. During the process, the LINCS WARNING occurs in
> the
> > initial procedures, I just decrease the timestep
> to
> > survive the MD. Is this correct?
> No, check your starting structure.
> 
> 
> > 
> > 
> > Thank you very much. 
> > 
> > Best
> > Tanping
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> -- 
> David.
>
________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular
> Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala
> University.
> Husargatan 3, Box 596,          75124 Uppsala,
> Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org  
> http://xray.bmc.uu.se/~spoel
>
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