[gmx-users] ewald,pme + bham potentials

[gmx at 4ka.mipt.ru]

On Wed, 21 Jan 2004 19:02:59 +0100
David <spoel at xray.bmc.uu.se> wrote:

> On Thu, 2004-01-22 at 10:51, gmx at 4ka.mipt.ru wrote:
> > On Wed, 21 Jan 2004 17:58:33 +0100
> > David <spoel at xray.bmc.uu.se> wrote:
> > 
> > > On Thu, 2004-01-22 at 09:23, 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
> > > > <>
> > > > 
> > > >  
> > > start by setting nstlog = 1
> > > and check the energies. WHich one is going berserk?
> > 
> > coulombtype=PME
> > 
> > >From md.log:
> > 
> >   Energies (kJ/mol)
> >      BuckingHam   Coulomb (SR)   Coulomb (LR)      Potential    Kinetic En.
> >    -4.38829e+04            NaN   -9.89192e+05            NaN            NaN
> >    Total Energy    Temperature Pressure (bar)
> >             NaN            NaN            NaN
> > 
> >            Step           Time         Lambda      Annealing
> >               1        0.00100        0.00000        1.00000
> > 
> >    Energies (kJ/mol)
> >      BuckingHam   Coulomb (SR)   Coulomb (LR)      Potential    Kinetic En.
> >             NaN            NaN            NaN            NaN            NaN
> >    Total Energy    Temperature Pressure (bar)
> >             NaN            NaN            NaN
> > 
> >            Step           Time         Lambda      Annealing
> >               2        0.00200        0.00000        1.00000
> > 
> >   <..>
> >   
> > > 
> > > Is it an infinite crystal (i.e. with PBC)?
> >   
> >  Yes, it is. 
> 
> The energy shows that it is the coulomb interactions. Do you have a
> number of exclusions set to something reasonable (2-3)? Are there
> chemical bonds between the atoms in your topology? Or constraints?

No bonds, no constrains.

My top:
[ defaults ]
 2 1 ; Buckingam potential
[ atomtypes ]
; name      mass   charge       ptype           c6            c12
 O      15.99940     -1.200         A           0.22617E-02   0.74158E-06        0.0000;
 Si     28.08000      2.400         A           0.14738E-01   0.22191E-04        0.0000;
[ nonbond_params ]
  O       O      2      1.339973E+5          27.6       1.688507E-2
  O      Si      2      1.737112E+6       48.7318       1.288457E-2
  Si     Si      2       0                      0               0
[ moleculetype ]
 O      0
[ atoms ]
 1       O      1       O        O      1       -1.2     15.99940
[ moleculetype ]
 Si     0;
[ atoms ]
 1       Si     1       Si      Si      2        2.4     28.08000
[ system ]
 Silica
[ molecules ]
O        750
Si       375