[gmx-users] zirconia
David van der Spoel
spoel at xray.bmc.uu.se
Fri May 18 10:22:36 CEST 2007
pushyami atluri wrote:
> hello,
> i am trying to simulate zirconia using buckhingham potentials but i get
> nan values for energies and also in the confout file.i would like to
> know if anybody has succeeded in simulating metallic systems with buck
> potentials because i came across this mailing list which talks about a
> problem being there with t code regarding the exponential term in buck
> potentials.please help
You have very large charges. Where does this potential come from? What
is the distance between atoms? If this is a bonded system then you can
not have such strong interactions at short distances.
> here is my top file
> please take some time to take a look in case i am goin wrong with t file
> ;topology file
> [ defaults ]
> 2
> [ atomtypes ]
> ;name mass charge ptype c6 c12
> OX 15.99940 -2.0 A 21.95e+05 0.01490 2.691e-03
> ZR 91.22420 4.0 A 0.0000000 1.00000 0.0000000
> [ nonbond_params ]
> ; i j func a b c6
> OX OX 2 21.95e+05 0.01490 2.691e-03
> ZR OX 2 9.512e+04 0.03760 0.0000000
> ZR ZR 2 0.0000000 1.00000 0.0000000
> [ moleculetype ]
> ZR 0
>
> [ atoms ]
> 1 ZR 1 DP ZR 1 4.0 91.22420
>
> [ moleculetype ]
> OX 0
>
> [ atoms ]
> 1 OX 1 DP OX 2 -2.0 15.99940
>
> [ system ]
> ZIRCONIA
>
> [ molecules ]
> ZR 2000
> OX 4000
>
> thanking you
>
> pushyami atluri
>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se
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