[gmx-users] ewald,pme + bham potentials

[David]

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?

> 
> > > 
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> > -- 
> > David.
> > ________________________________________________________________________
> > 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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-- 
David.
________________________________________________________________________
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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