<div dir="ltr"><div><div><div><div><div><div><div><div>Hi all,<br><br></div>I'll try to explain to you my situation.<br>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.<br></div>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.<br></div>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.<br></div><br></div>The electrostatic configuration that I use in the .mdp file is the following:<br><span style="font-family:courier new,monospace"><br>coulombtype = cut-off<br>rlist = 0<br>rcoulomb = 0.9<br>rvdw = 0.9</span><br><br></div>And here some lines of the mdp.log that might be of interest:<br><span style="font-family:courier new,monospace"><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</span><br><br></div>Thank you very much in advance.<br><br>Iñigo Sáenz<br></div>Universitat Pompeu Fabra, Barcelona.<br><div><div><br><div><div><br><br></div></div></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">2014-10-10 14:40 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>
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.<span class="HOEnZb"><font color="#888888"><br>
<br>
Berk</font></span><div><div class="h5"><br>
<br>
On 10/10/2014 02:37 PM, Mark Abraham wrote:<br>
</div></div></div><div><div class="h5">
<blockquote type="cite">
<div dir="ltr">Hi,
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Mark</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, Oct 10, 2014 at 12:53 PM, IÑIGO
SAENZ <span dir="ltr"><<a href="mailto:inigo.saenz01@estudiant.upf.edu" target="_blank">inigo.saenz01@estudiant.upf.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div>
<div>Hi,<br>
<br>
</div>
Does anyone know in which .C file are the LJ and Coulomb
short range interactions energies calculated, please?<br>
I'm getting crazy studying the gromacs' source code and
I cannot find the right .C file where those calculations
are made.<br>
<br>
Iñigo Sáenz<br>
</div>
Universitat Pompeu Fabra, Barcelona.<br>
</div>
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