[gmx-users] a question

[David van der Spoel]

On Fri, 2003-08-22 at 10:32, Yuguang Mu wrote:
> We have two complied versions of gromacs, one is complied by intel fortran
> 7.0, one is complied g77
> 
> I check different water models,
> 
> one is spc, one is tip3p amber model with  1146 water molecules in each
> case (with PME cutoff 1.0)
> 
> By using the intel fortran versions
> 
> for spc such line is printed out
>  ***************************************************************
>  Going to use C-settle (573 waters)
>  wo = 0.888096, wh =0.0559521, wohh = 18.0154,
>  rc = 0.081665, ra = 0.00645837 rb = 0.051255, rc2 = 0.16333,
>  rone = 1, dHH = 0.16333, dOH = 0.1
>  ***************************************************************
> 
> the average density turns out to be  966
> 
> for tip3p such line is printed out
> ********************************************************
> Going to use C-settle (9781 waters)
> wo = 0.888099, wh =0.0559503, wohh = 18.016,
> rc = 0.075695, ra = 0.00655606 rb = 0.0520322, rc2 = 0.15139,
> rone = 1, dHH = 0.15139, dOH = 0.09572
> **********************************************************
> 
> the average density turns out to be  986
> (exactly as the amber sander results)
In both case above you use the C version of the routines, and you see
that the different models are represented correctly and hence you get
the correct results.


> 
> which mean that it do simulated using different water model.
> 
> 
> But when I use g77 version,
> no "Going to use C-settle (573 waters)" line appears.
> the different water model simulations nearly give the same density:
> 966 , which turns out that it cannot use correctly the other water model.
Now when you use the fortran version no such information is printed, but
it should still work. 

Could you specify how you compiled the programs?
(configure command + environment variables + make command).

On x86 architecture it does not make sense to use fortran (except,
maybe, when using double precision on Pentium 3 or Athlon), because the
assembly loops are faster anyway. The Intel compiler should produce
slightly faster code for things like shake/settle etc.

-- 
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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