David van der Spoel
spoel at xray.bmc.uu.se
Thu Feb 20 18:57:32 CET 2003
On Thu, 2003-02-20 at 16:28, Dmytro wrote:
> I'm prepearing the system for simulation. After genbox I'm doing md with
> posres of protein atoms. From the very begining solvent rapidly
> desrease its own volume and becomes more dence. In my box holes start to
> appear ! Genbox generated solvent molecules with default pressure.
> I'didn't used pressure coupling in the posres. What it coulbd be related
What's the density? If it is too low density solvent will cluster
together. You have to do p coupling to get the right density.
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Dr. David van der Spoel, Dept. of Cell & Mol. Biology
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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