[gmx-users] ewald,pme + bham potentials

[gmx at 4ka.mipt.ru]

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. 

> > 
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> -- 
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.