[gmx-users] graphite

[David van der Spoel]

On Thu, 2003-07-31 at 11:43, Yuguang Mu wrote:
> Hi David,
> What use is the environment variable:
>  setenv GMXFULLPBC 1
> 
> Does it means that the cutoff can be larger than the half of a box ?
> Can it be used in Gromacs 3.1.4 ?
yes,

it means that infinite systems can be treated as well, because gmx
computes the periodicity for each interaction separately instead of once
per molecule (which is faster).
> 
> 
> Dr. Yuguang Mu
> Institute for Physical and Theoretical Chemistry
> J.W. Goethe University Frankfurt am Main
> Marie Curie Str. 11
> 60439 Frankfurt/Main, Germany
> Tel: +49-(0)69-798-29711
> 
> On 31 Jul 2003, David van der Spoel wrote:
> 
> > 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 Iÿm confused
> > > that it is OK if I put the graphite into vacuum without water and
> > > simulate it. I donÿt know why the water will affect the graphiteÿs 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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-- 
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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