[gmx-developers] Lennard Jones and Electrostatic energies.

[IÑIGO SAENZ]

Hi all,

I'll try to explain to you my situation.
I have a simple system of 3000 Argon atoms without bonds, without angles,
without dihedrals, only with LJ parameters and I run it with ACEMD and I
obtained a VDW potential of -1.34 KJ/mol.
After this, I generate the same system for running in gromacs (.top and
.gro files), I run it and I obtain a LJ energy of -1.32524.
What I want is to include some print statements into the source files of
gromacs in order to be able to analyze how gromacs performs the calculation
of LJ potential to find where the desviation in the results between ACEMD
and GROMACS is produced.

The electrostatic configuration that I use in the .mdp file is the
following:

coulombtype = cut-off
rlist                    = 0
rcoulomb                 = 0.9
rvdw                     = 0.9

And here some lines of the mdp.log that might be of interest:

Gromacs version:    VERSION 5.0.1
Precision:          single
Memory model:       64 bit
MPI library:        thread_mpi
OpenMP support:     enabled
GPU support:        disabled
invsqrt routine:    gmx_software_invsqrt(x)
SIMD instructions:  AVX_256

Thank you very much in advance.

Iñigo Sáenz
Universitat Pompeu Fabra, Barcelona.




2014-10-10 14:40 GMT+02:00 Berk Hess <hess at kth.se>:

>  Hi,
>
> We might need a wiki entry for this, since this is a question that keeps
> popping up, but it's unfortunately not easy to answer.
>
> Berk
>
>
> On 10/10/2014 02:37 PM, Mark Abraham wrote:
>
> Hi,
>
>  The simple answer is "in most of them" :-) The non-bonded kernels where
> they are computed come in lots of physics and hardware flavours, and then
> there is a lot infrastructure that coordinates accumulating them properly.
> We can point you in the right direction if we know what you're trying to
> achieve, though.
>
>  Mark
>
> On Fri, Oct 10, 2014 at 12:53 PM, IÑIGO SAENZ <
> inigo.saenz01 at estudiant.upf.edu> wrote:
>
>>  Hi,
>>
>>  Does anyone know in which .C file are the LJ and Coulomb short range
>> interactions energies calculated, please?
>> I'm getting crazy studying the gromacs' source code and I cannot find the
>> right .C file where those calculations are made.
>>
>> Iñigo Sáenz
>>  Universitat Pompeu Fabra, Barcelona.
>>
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>
>
>
>
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