[gmx-developers] innerloop code

David van der Spoel spoel at xray.bmc.uu.se
Sat Sep 2 09:58:49 CEST 2006

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)

> Thanks a lot!!
> -Chenyue
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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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