[gmx-developers] Wall interaction with tabulated potential

Jakub Krajniak jakub.krajniak at cs.kuleuven.be
Sat Feb 27 09:12:26 CET 2016

On 2016-02-05 09:57, Sudharsan Pandiyan wrote:
>/Dear Gmx developers, />//>/I am trying to simulate a wall option using tabulated potentials />/option. But it gives different LJ potential values when I compare 12-6 />/potential with the tabulated potential (where the table was generated />/using same sigma and epsilon values that were used for 12-6 potential). />//>/I intend to modify my table potential later so I wanted to make sure />/that it produces correct result. But my test shows that there is a />/difference between 12-6 and tabulated potentials for wall interaction. />/Could you please explain what is the difference and how can I get the />/correct potential energy for tabulated potentials? />//>/PS: In the manual, its written that both 9-3 and 10-4 are integrated />/over the surface area and 12-6 potential was applied directly with the />/z-distance. But how the tabulated potential is represented? (section />/7.3.20) />//>//

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.

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:

I don't know if you are using GitHub pull request so I attached patch to this message.
It's also on github branch:

Best regards,

Jakub Krajniak
KU Leuven, Dept. Computer Science lokaal: 01.41
+32 477 68 84 04 / +32 16 37 39 92

Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20160227/061d7ab9/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 0001-This-fixes-the-issue-with-tabulated-wall-potential.patch
Type: text/x-patch
Size: 2812 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20160227/061d7ab9/attachment.bin>

More information about the gromacs.org_gmx-developers mailing list