ygmu at theochem.uni-frankfurt.de
Thu Jul 31 11:45:01 CEST 2003
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 ?
Dr. Yuguang Mu
Institute for Physical and Theoretical Chemistry
J.W. Goethe University Frankfurt am Main
Marie Curie Str. 11
60439 Frankfurt/Main, Germany
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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