[gmx-developers] Modification of calculation of the force

Mark Abraham Mark.Abraham at anu.edu.au
Thu Aug 13 03:03:37 CEST 2009

Camilo Andrés Jimenez Cruz wrote:
> Hi!
> Pieter, thanks for the hint.  I tried simulating a box with just TIP3P
> water by using this option, but the results I get for energy  and
> structure (rdf) are very different to the ones I get without this
> option. Is there something I am missing out?
> By the way, I am required now to implement the changes in gromacs
> v3.3.3, so I am looking at the code in gmxlib/nonbonded/nonbonded.c.
> So far, I get that, the function to change is the one pointed by
> kernelptr, and that those functions are written in assembler for each
> architecture. But I haven't been able to find which one of the
> assembler codes for my architecture
> (/data/gaia-disk05/jimenc/AcceleratedMolecularDynamics/local/gromacs/src/gromacs-3.3.3/src/gmxlib/nonbonded/nb_kernel_x86_64_sse)
> is the one being executed. Is there an easy way to find this out?

Seriously, as I said last time, you are very likely to get better speed 
and faster development from using the tabulated interactions. (... as 
long as your potential is a simple function of distance between the 


> Thanks in advance!
> On Sun, Aug 9, 2009 at 4:21 AM, Pieter van 't
> Hof<pieter.van.t.hof at logica.com> wrote:
>> Hi,
>> In Gromacs 4 you can set the environment variable GMX_NB_GENERIC (using
>> in bash:$ export GMX_NB_GENERIC=1)
>> Then plain C loops in src/gmxlib/nonbonded/nb_generic.c will be used.
>> This is where the forces per atom are calculated. From there on you can
>> implement the function you want.
>> On Sat, 2009-08-08 at 17:22 -0400, Camilo Andrés Jimenez Cruz wrote:
>>> Hi everybody.
>>> I would like your advise in modifying the source code of gromacs, in
>>> such a way that the force is calculated by using a modified potential
>>> that goes like V' = V + function(V), where function(V) is a simple
>>> function of V (or Force = Force + function(Force)).
>>> I just started checking the code, but I thought your help could save
>>> me many days.
>>> I am using gromacs-4.0.5, but I don't have a requirement to stick to
>>> this version.
>>> Thanks in advance!
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