[gmx-users] ewald,pme + bham potentials
spoel at xray.bmc.uu.se
Wed Jan 21 19:52:00 CET 2004
On Wed, 2004-01-21 at 19:05, Lianqing Zheng wrote:
> For me, the best result was the cell exploded in seveval steps. Do you use
> BKS potential? I think a possible reason is in the potential itself:
> U->-inf when r->0. And there is probably no easy way to add an 30-6 LJ
> potential to fix this glitch in Gromacs.
If I'm not totally wrong you can use table lookups with Buckingham as
well. Don't know how exactly though...
> On Thu, 22 Jan 2004 gmx at 4ka.mipt.ru wrote:
> > Hello.
> >I've spent some days trying to make simulations in sio2
> >using Bham potentials with ewald,pme but without success (I've told about my attempts before ).
> >Just wonder, have anybody simulated systems with such combinations of
> >potentials and calculation algorithms before and got positive results?
> >If so, I'll go on in my attempts, if not -- give up.
> >System always fails on first step and mdrun dumpes core with Ewald or
> >writes bad values to the out.gro at last step ( i used nsteps=1,2 ):
> > 1115Si Si 1115 NaN NaN NaN NaN NaN NaN
> > 1116Si Si 1116 NaN NaN NaN NaN NaN NaN
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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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