[gmx-users] PME in water

[Erik Lindahl]

Does it work when you are not using PME?

If yes, how did you compile FFTW? Try using gcc and a low optimization  
level there too!

Cheers,

Erik

On Monday, May 5, 2003, at 18:59 America/Los_Angeles, Lianqing Zheng  
wrote:

> 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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>
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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