[gmx-users] infinite systems

[David]

On Fri, 2003-08-08 at 19:50, Yuguang Mu wrote:
> Dear David,
> I want to simulate  an infinite system, a small peptide in water
> the system is quite small, total 200 atoms.
> if I use normal cut-off, the rcut  has to be smaller than box/2 (around 5
> A), then the simulated system is nonphysical, due to the small cutoff.
> I try to use setenv GMXFULLPBC 1, as:  export GMXFULLPBC=1, then use
> rcut=1nm .
> But the grompp still say it is a error : rcut > box/2.
> What should I do ?

set 
pbc = no
in mdp file
> 
> 
> 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 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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> > >
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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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > _______________________________________________
> > gmx-users mailing list
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> >
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular 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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