[gmx-users] PME in water

David van der Spoel spoel at xray.bmc.uu.se
Tue May 6 09:01:02 CEST 2003

On Tue, 2003-05-06 at 07:59, Lianqing Zheng wrote:
> Thanks Erik! I recompiled FFTW with gcc. PME is working for water now. But
> I still need to set fr->tabscale_exp=fr->tabscale to use Buckingham
> potential. 
> However, I got another problem: the simulation cell exploded at the first
> time step:
>    Energies (kJ/mol)
>      BuckingHam   Coulomb (SR)   Coulomb (LR)      Potential    Kinetic
> En.
>     8.67478e+04   -4.14156e+07   -1.27296e+06   -4.26018e+07
> 8.90925e+07
>    Total Energy    Temperature Pressure (bar)
>     4.64907e+07    4.65377e+06   -1.09662e+06
> Step 1  Warning: pressure scaling more than 1%, mu: 0.967101 0.967101 0.967101
> Large VCM(group rest):    -10.41395,     -2.04940,    -33.29021, ekin-cm:
> 18777794.00000
> I used Berendsen NPT ensemble and change tau_t, tau_p from 0.1 to 1.0, but
> it didn't make much difference. EM did not help either. But it runs fine
> with Cut-off Coulomb option.
I would like to suggest you recompile evrything (LAM, FFTW, GROMACS)
with the Sun C compiler but with the -g flag. If you then still have
problems it should be possible to deduce whether it is GROMACS or the
compiler. If it works you can slowly increase the optimzation level.

I don't know whether this applies to Sun machines, but I have seen on an
IBM, that if you optimize one piece of code (e.g. FFTW) for one
processor type, and another for another, you can not mix them, that is,
the compiler will link it, but executables will crash.

Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
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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