[gmx-developers] Modification of calculation of the force

[Camilo Andrés Jimenez Cruz]

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?

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