<div dir="ltr"><div><div><div>Thanks to all!!!<br></div>Your help has been very valuable for me. I was stuck with this problem and now I know how to continue.<br></div>You will read me again if I have got new questions (Sure I will have :) ).<br><br></div>Thanks!<br></div><div class="gmail_extra"><br><div class="gmail_quote">2014-10-13 12:50 GMT+02:00 Berk Hess <span dir="ltr"><<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<div>Hi,<br>
<br>
This issue was already resolved, but somehow my answer didn't go
to the list.<br>
<br>
Using vdw-modifier=none made the energy match ACEMD. Apparently
ACEMD doesn't correct for the jump in the LJ energy at the
cut-off.<br>
<br>
Cheers,<br>
<br>
Berk<div><div class="h5"><br>
<br>
On 10/10/2014 07:21 PM, Mark Abraham wrote:<br>
</div></div></div><div><div class="h5">
<blockquote type="cite">
<div dir="ltr"><br>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, Oct 10, 2014 at 4:27 PM,
Szilárd Páll <span dir="ltr"><<a href="mailto:pall.szilard@gmail.com" target="_blank">pall.szilard@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
I think you'll have the easiest time with the plain C
reference<br>
kernels; the actual kernels used in production are
compiled from SIMD<br>
intrinsics code which you likely don't want to start
reading (and from<br>
where you can't even print).<br>
<br>
For the Verlet cut-off scheme (default in 5.0) these are
the files<br>
with the reference implementation you should be looking
at:<br>
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref{,_inner,_outer}.c/h<br>
- there is no single source file, but this should be quite
easy to read.<br>
There is a bit more readable GPU reference kernel (trigger
with<br>
GMX_EMULATE_GPU env. var.):<br>
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.c<br>
Finally, for the group scheme there's also self-contained
reference kernel here:<br>
src/gromacs/gmxlib/nonbonded/nb_generic.c<br>
<br>
The first and last kernels for the CPU Verlet and Group
scheme you can<br>
trigger with the GMX_DISABLE_SIMD_KERNELS environment
variable.<br>
<br>
Cheers,<br>
--<br>
Szilárd<br>
<br>
PS: make sure that the same interaction modifiers (switch,
shift) are<br>
used by both GROMACS and ACEMD.<br>
</blockquote>
<div><br>
</div>
<div>Szilard's point here is really important. Some quality
time with the docs of both packages is always needed to
try to get them to do exactly the same thing as each
other. Ultimately they can't do the addition of a large
bunch of floating-point numbers in exactly the same way,
but you need to make sure all the non-bonded settings are
really the same.</div>
<div><br>
</div>
<div>Also, start by verifying the LJ potential between two
atoms, because now there's no accumulation to have
different behaviour ;-) Then, observe how much the
potential in each code varies even upon "invariant"
operations, like a rotation of the entire system (which
will change the order of the accumulation). By now, maybe
you've observed that the deviation is of an expected
magnitude (YMMV, I have no idea).</div>
<div><br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
On Fri, Oct 10, 2014 at 4:07 PM, IÑIGO SAENZ<br>
<div>
<div><<a href="mailto:inigo.saenz01@estudiant.upf.edu" target="_blank">inigo.saenz01@estudiant.upf.edu</a>>
wrote:<br>
> Hi all,<br>
><br>
> I'll try to explain to you my situation.<br>
> I have a simple system of 3000 Argon atoms
without bonds, without angles,<br>
> without dihedrals, only with LJ parameters and I
run it with ACEMD and I<br>
> obtained a VDW potential of -1.34 KJ/mol.<br>
> After this, I generate the same system for
running in gromacs (.top and .gro<br>
> files), I run it and I obtain a LJ energy of
-1.32524.<br>
> What I want is to include some print statements
into the source files of<br>
> gromacs in order to be able to analyze how
gromacs performs the calculation<br>
> of LJ potential to find where the desviation in
the results between ACEMD<br>
> and GROMACS is produced.<br>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>You could do this, but the different order of
operations in the two codes is going to make it hard to
get meaningful output to compare.</div>
<div><br>
</div>
<div>Mark</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div>
><br>
> The electrostatic configuration that I use in the
.mdp file is the<br>
> following:<br>
><br>
> coulombtype = cut-off<br>
> rlist = 0<br>
> rcoulomb = 0.9<br>
> rvdw = 0.9<br>
><br>
> And here some lines of the mdp.log that might be
of interest:<br>
><br>
> Gromacs version: VERSION 5.0.1<br>
> Precision: single<br>
> Memory model: 64 bit<br>
> MPI library: thread_mpi<br>
> OpenMP support: enabled<br>
> GPU support: disabled<br>
> invsqrt routine: gmx_software_invsqrt(x)<br>
> SIMD instructions: AVX_256<br>
><br>
> Thank you very much in advance.<br>
><br>
> Iñigo Sáenz<br>
> Universitat Pompeu Fabra, Barcelona.<br>
><br>
><br>
><br>
><br>
> 2014-10-10 14:40 GMT+02:00 Berk Hess <<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>>:<br>
>><br>
>> Hi,<br>
>><br>
>> We might need a wiki entry for this, since
this is a question that keeps<br>
>> popping up, but it's unfortunately not easy
to answer.<br>
>><br>
>> Berk<br>
>><br>
>><br>
>> On 10/10/2014 02:37 PM, Mark Abraham wrote:<br>
>><br>
>> Hi,<br>
>><br>
>> The simple answer is "in most of them" :-)
The non-bonded kernels where<br>
>> they are computed come in lots of physics and
hardware flavours, and then<br>
>> there is a lot infrastructure that
coordinates accumulating them properly.<br>
>> We can point you in the right direction if we
know what you're trying to<br>
>> achieve, though.<br>
>><br>
>> Mark<br>
>><br>
>> On Fri, Oct 10, 2014 at 12:53 PM, IÑIGO SAENZ<br>
>> <<a href="mailto:inigo.saenz01@estudiant.upf.edu" target="_blank">inigo.saenz01@estudiant.upf.edu</a>>
wrote:<br>
>>><br>
>>> Hi,<br>
>>><br>
>>> Does anyone know in which .C file are the
LJ and Coulomb short range<br>
>>> interactions energies calculated, please?<br>
>>> I'm getting crazy studying the gromacs'
source code and I cannot find the<br>
>>> right .C file where those calculations
are made.<br>
>>><br>
>>> Iñigo Sáenz<br>
>>> Universitat Pompeu Fabra, Barcelona.<br>
>>><br>
>>> --<br>
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>>><br>
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</blockquote>
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<br>
</div>
</div>
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