[gmx-users] PME in water

[Lianqing Zheng]

Hi, Erik:

Thanks for you suggestions! I change CC to gcc and re-compile Gromacs.
Something did change. Although I did get arithmetic exception this time, a
segmentation fault error occurred in low_constrain (). And the value of d2
was still strangely large sometimes even though no arithmetic exception
was displayed.

For the SiO2 system, I didn't get arithmetic exception either, but
tabscale for EXP tern was still zero:
Generated table with 900 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 900 data points for EXPMIN.
Tabscale = 0 points/nm

With coulombtype = Ewald, I got Coulomb (SR)=NaN. If I add a line before
the use of init_table():
fr->tabscale_exp=fr->tabscale;
It produced a number, which was different from the one from Moldy or my
code. For PME, it got a segmentation fault in do_inputrec ().

Any insight? Thank you very much!

Lianqing

On Mon, 5 May 2003, Erik Lindahl wrote:

>Hi,
>
>This could be a compiler and/or optimization problem. I would try to  
>rule this out by:
>
>1. Compiling without optimization. See the FAQ online for setting your  
>own CFLAGS.
>2. Use gcc instead of the Sun compiler.
>
>If either of these options make it work we'll have to search for a bug  
>with the Sun compiler...
>
>Cheers,
>
>Erik
>
>On Monday, May 5, 2003, at 15:49 America/Los_Angeles, Lianqing Zheng  
>wrote:
>
>> Dear Gromacs pals:
>>
>> I didn't succeed to use PME in the water system under the "tutor"
>> directory. The only modification I did in water.mdp was adding a PME  
>> line:
>> coulombtype         = PME
>>
>> The error was arithmetic exception (again) occurring at solve_pme() in
>> pme.c. When kx=0, ky=0, kz=5, I got the following d1 and d2:
>> d1=0.238266,d2=-113907695932561209218061626031210496.000000
>>
>> Have you got the similar error? My machine is Sun Solaris2.8. Gromacs
>> version is 3.1.4.
>>
>> Thank you very much for your kind help!
>>
>> Lianqing
>>
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>------------------------------------------------------------------------ 
>-----
>Erik Lindahl, MSc, PhD     <lindahl at stanford.edu>
>D109, Fairchild Building
>Dept. Structural Biology, Stanford University School of Medicine
>Tel. 650-7250754    Fax. 650-7238464
>
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