[gmx-developers] innerloop code

[Chenyue Xing]

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?

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> 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
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