[gmx-developers] inner loop and lennard-jones

Erik Lindahl lindahl at stanford.edu
Sun May 4 09:34:56 CEST 2003

Hi Daniele,

First, check the flopcount statistics at the end of your run for a  
summary of which innerloops were used. Then check  
gromacs/include/types/nrnb.h for an explanation of the innerloop  

The 1,4-interactions are always tabulated for performance reasons  
(inl3300), but that loop might not be used for the normal nonbonded  

You should also be aware that we use assembly loops on x86 hardware;  
you can turn them off by setting the variable NOASSEMBLYLOOPS before  
starting mdrun.



On Wednesday, Apr 30, 2003, at 10:37 US/Pacific, Daniele Bemporad wrote:

> Hi all.
> I need to hack the gromacs code and modify the lennard-jones  
> potential. I
> have added print statements in each inner loop to see which of them was
> involved in my simulation and to check the value of relevant variables.
> In particular, it has turned out that the inner loop involved is the
> inl3300. However, only the 1-4 interactions are printed out and there  
> is
> no way to find where and when the other non-bonded interactions are
> calculated. Can anybody be of any help?
> Thanks a lot
> Daniele Bemporad
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Erik Lindahl, MSc, PhD     <lindahl at stanford.edu>
D109, Fairchild Building
Dept. Structural Biology, Stanford University School of Medicine
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