David van der Spoel
spoel at xray.bmc.uu.se
Fri Oct 19 21:08:02 CEST 2001
On Fri, 19 Oct 2001, Andrew Horsfield wrote:
>I am trying to use something other than the cutoff for electrostatics. The
>key facts of the simulation are:
>1) CG relaxation
>2) Net charge on unit cell (-12)
>3) 5805 atoms (including solvent)
>4) I am using PC running Linux (2.4 kernel, RH 7.1)
>And I observe:
>a) Ewald causes a core dump.
>b) PME give the following output:
>> Starting Energy = -5.499808236450613e+04
>> F-Norm = nan
>> Fatal error: ci = -2147483648 should be in 0 .. 391 [FILE nsgrid.c, LINE 214]
>Is there something I am doing wrong?
To check quickly whether it is the charge you can ofcourse replace 12
solvents by Na+ (using genion).
>I realize that a net charge for periodic systems leads to infinite
>energies, but I assume this is all taken care of in the G=0 term of the
>FFT's. Is this correct?
I'm not sure to be honest. The 0,0,0 term is not taken into account in
computation of forces and charges.
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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