Re: Another question about MD simulation of a domain.

From: \ (jonathan_at_ibt.unam.mx)
Date: Tue Sep 27 2005 - 14:15:59 CDT

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Are you overlapping the protein onto the solvent molecules? If you
preequilibrated the water molecules, there is probably no void in the water box
to fit the solute in.

J. Valencia

Quoting Boyang Wang <pkuwangboyang_at_yahoo.com.cn>:

> Hi all. Another question is, if I put a domain in a solvent box, with
> the solvent preequilibrated, and start the simulation, why is the energy
> suddenly extremely high? Shall I add ions of a buffer solution? I just
> don't know how to solve the charge problems, and how to start the
> simulation of a given protein structure.
>
> Thanks.
> Boyang.
>
>
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