[gmx-users] Re:help!!! "can not fix pbc"
David van der Spoel
spoel at xray.bmc.uu.se
Mon Feb 23 09:16:01 CET 2004
On Mon, 2004-02-23 at 02:07, Wei Fu wrote:
> Hi, David,
> I use GROMACS3.2. I also check energy and temprature, both of them are
> OK. I think, maybe the structure is not well optimized, so I use cg
> algorithm continue optimize the strucre (set emtol = 300), but this time,
> when I heat the protein, it generates the step?.pdb coordinate. How shold
> I fix this?
> In addition, I set pressure with following parameter:
> Pcoupl = berendsen
> tau_p = 1
> compressibility = 4.5e-5
> ref_p = 1.0
> Since I already optimize the system well, why it still geneartes
you say nothing about what type of system it is. Try tau_p = 5
> Thanks for your help,
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David van der Spoel, PhD, Assist. 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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