[gmx-developers] Modification of calculation of the force

Camilo Andrés Jimenez Cruz camilo.jimenezc at gmail.com
Wed Aug 12 17:04:55 CEST 2009


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
is the one being executed. Is there an easy way to find this out?

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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Camilo Andrés Jiménez Cruz

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