[gmx-developers] innerloop code

[David van der Spoel]

Chenyue Xing wrote:
> Hi David,
>  
> Thank you for your quick reply.
> I tried setenv and compared 2 simulations with exactly the same initial 
> structure and parameters (one w/ NOASSEMBLYLOOPS, one w/o it)
> But the results seem to be different. Is this normal?

yes if the simulation is long enough. you don't say how long yours is, 
but round-off errors will cause drift even for codes that are 
mathematically identical. You can try running in double precision and 
differences will be less.

the assembly source is in src/gmxlib/nonbond/*


>  
> Here's my data:
> initial structure:
> Testing 3 particles (particle 2W,3W are positionally fixed)
>     3
>     1W        W    1   3.237   3.574   3.584  0.0000  0.0000  0.5000
>     2W        W    2   3.637   3.574   5.000  0.0000  0.0000  0.0000
>     3W        W    3   2.637   3.574   0.000  0.0000  0.0000  0.0000
>    6.00000   6.00000   6.00000
>  
> w/o NOASSEMBLYLOOPS final structure
> testing 3 particles
>     3
>     1W        W    1   5.109   3.574   4.720  0.0690  0.0000  0.3215
>     2W        W    2   3.637   3.574   5.000  0.0000  0.0000  0.0000
>     3W        W    3   2.637   3.574   0.000  0.0000  0.0000  0.0000
>    6.00000   6.00000   6.00000
>  
> w/ setenv NOASSEMBLYLOOPS 1 final structure
> testing 3 particles
>     3
>     1W        W    1   5.561   3.574   2.893 -0.2213  0.0000 -0.2213
>     2W        W    2   3.637   3.574   5.000  0.0000  0.0000  0.0000
>     3W        W    3   2.637   3.574   0.000  0.0000  0.0000  0.0000
>    6.00000   6.00000   6.00000
> (I assume w/ NOASSEMBLYLOOPS 1, it runs w/ c codes?)
> 
>  
> Also, if I have assemblyloops enabled (not setting noassemblyloops 1), 
> can I actually find those assembly codes to read?
>  
> Thank you very much again!
>  
>  
> On 9/2/06, *David van der Spoel* <spoel at xray.bmc.uu.se 
> <mailto:spoel at xray.bmc.uu.se>> wrote:
> 
>     Chenyue Xing wrote:
>      > Hi all,
>      >
>      > I'm trying to make the nonbonded interaction between 2 particles
>     (let's
>      > say 2 water particles for now) z-dependent only. So I went into the
>      > innerloop code (v3.3.1) to change rsq to "rsq = dz*dz". I changed
>     this
>      > in mknb_innerloop.c so that it automatically updates all the
>     nb_kernel
>      > files when being compiled. However, this doesn't seem to have
>     different
>      > results from the original r-dependent interation. (meaning, with the
>      > same initial conditions, the systems ended up in the same final
>     conditions)
>      >
>      > That sounds like not nb_kernelxxx_c.c codes are being used when doing
>      > simulations.
>      > Can any expert help me with this issue?
>      > If it's sth related Gromacs compiled w/ assembly compiler, how can
>      > disable asm for now? (guess I won't anyway be able to change any ASM
>      > related stuff)
> 
>     setenv NOASSEMBLYLOOPS 1
>      >
>      > Thanks a lot!!
>      >
>      > -Chenyue
>      >
>      >
>      >
>     ------------------------------------------------------------------------
> 
>      >
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> 
>     --
>     David.
>     ________________________________________________________________________
>     David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>     Dept. of Cell and Molecular Biology, Uppsala University.
>     Husargatan 3, Box 596,          75124 Uppsala, Sweden
>     phone:  46 18 471 4205          fax: 46 18 511 755
>     spoel at xray.bmc.uu.se
>     <mailto:spoel at xray.bmc.uu.se>    spoel at gromacs.org
>     <mailto:spoel at gromacs.org>   http://folding.bmc.uu.se
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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://folding.bmc.uu.se
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