[gmx-users] graphite

[David van der Spoel]

On Thu, 2003-07-31 at 10:38, Yonggang Gao wrote:

> 
> Hi Anton,
> 
>  
> 
> I just select one layer graphite about 432 carbon atoms as solute, and
> the simulation is error when I put it into the water and make it
> equilibrium. Certainly I have done the minimization. And I’m confused
> that it is OK if I put the graphite into vacuum without water and
> simulate it. I don’t know why the water will affect the graphite’s 1-4
> interaction. I try to select two layer graphite about 864 atoms, and
> the same problem. Could you help me?
> 
>  
> 
> Thanks a lot.


is this a periodic system? In that case you may want to set an
environment variable:
setenv GMXFULLPBC 1

and rerun
> 
>  
> 
>  
> 
> Yonggang
> 
>  
-- 
Groeten, David.
________________________________________________________________________
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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