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

David spoel at xray.bmc.uu.se
Sun Jul 31 12:45:54 CEST 2005

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?

> 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

> 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 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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