[gmx-users] Re:help!!! "can not fix pbc"

[David van der Spoel]

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
> step?.pdb 

you say nothing about what type of system it is. Try tau_p = 5

> 
> Thanks for your help, 
> 
> Cheers,
> 
> Wei
> 
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-- 
David.
________________________________________________________________________
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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