<html>
<head>
<meta http-equiv="content-type" content="text/html; charset=utf-8">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<pre style="white-space: pre-wrap; color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; widows: 1; word-spacing: 0px; -webkit-text-stroke-width: 0px;">On 2016-02-05 09:57, Sudharsan Pandiyan wrote:
><i> Dear Gmx developers,
</i>><i>
</i>><i> I am trying to simulate a wall option using tabulated potentials
</i>><i> option. But it gives different LJ potential values when I compare 12-6
</i>><i> potential with the tabulated potential (where the table was generated
</i>><i> using same sigma and epsilon values that were used for 12-6 potential).
</i>><i>
</i>><i> I intend to modify my table potential later so I wanted to make sure
</i>><i> that it produces correct result. But my test shows that there is a
</i>><i> difference between 12-6 and tabulated potentials for wall interaction.
</i>><i> Could you please explain what is the difference and how can I get the
</i>><i> correct potential energy for tabulated potentials?
</i>><i>
</i>><i> PS: In the manual, its written that both 9-3 and 10-4 are integrated
</i>><i> over the surface area and 12-6 potential was applied directly with the
</i>><i> z-distance. But how the tabulated potential is represented? (section
</i>><i> 7.3.20)
</i>><i>
</i>><i>
</i>
Hi,
I've looked into the code and I might find the solution for this problem.
I've run NVE simulation for very simple LJ systems of two particles
and the single particle with the wall and I compared the energies and the trajectories.
Tests:
1. two LJ particles at z-distance 1.2 (parametrize LJ interaction): -0.235941 kJ/mol
2. two LJ particles at z-distance 1.2 (interaction from table6-12.xvg): -0.23594 kJ/mol
and wall (after fix):
3. particle at distance 1.2 from the wall (wall-type 12-6): -0.235892 kJ/mol
4. particle at distance 1.2 from the wall (wall-type table table6-12.xvg
): -0.235893 kJ/mol
the data from 10000 steps. The simulation files are here:
<a class="moz-txt-link-freetext" href="https://www.dropbox.com/s/ryr0x7q974gefu6/experiment.zip?dl=0">https://www.dropbox.com/s/ryr0x7q974gefu6/experiment.zip?dl=0</a>
I don't know if you are using GitHub pull request so I attached patch to this message.
It's also on github branch:
<a class="moz-txt-link-freetext" href="https://github.com/MrTheodor/gromacs/tree/fix_wall">https://github.com/MrTheodor/gromacs/tree/fix_wall</a>
Best regards,
Jakub</pre>
<pre class="moz-signature" cols="72">--
Jakub Krajniak
KU Leuven, Dept. Computer Science lokaal: 01.41
+32 477 68 84 04 / +32 16 37 39 92</pre>
<br>
<FONT FACE=3D"Helvetica" SIZE=3D2>Disclaimer: <A HREF="http://www.kuleuven.be/cwis/email_disclaimer.htm">http://www.kuleuven.be/cwis/email_disclaimer.htm</A> for more information.</FONT>
<BR>
</body>
</html>