[gmx-users] How to turn off LJ interaction between two groups?

Hu Zhongqiao zhongqiao_hu at nus.edu.sg
Thu Jan 7 15:18:55 CET 2010

Dear all,


I want to make an ideal semipermeable membrane comprised of several
hundreds of atom CM in a plane, which is fully permeable to water but
resistant to NaCl. I defined atomtype CM (CM is neutral)

[ atomtypes ]

  CM     6  12.01      0.000     A  2.22343e-03   3.434770e-06


In order to turn off the LJ interaction between CM and H2O, I specified

[ nonbond_params ]

; i    j func          c6           c12

   OW    CM     1 0.0000000e-03  0.00000e-06


After I make a system (SOL phase + semipermeable membrane + NaCl phase),
I run energy minimization. But after EM, I found there is an obvious
space between SOL phase (or NaCl phase) and membrane. In the initial
structure, this pace does not exist. So it means that this membrane
still has LJ interaction with SOL. I also use g_energy command to check
the LJ_SR interaction between membrane and SOL, the obtained LJ_SR
interaction energy is not equal to zero.


Why do membrane and SOL still have LJ interaction when I turn off it in
my topology file? What is the correct step to turn off LJ interaction
between two groups?


Best wishes,



Dept of Chem & Biomole Engin

National University of Singapore



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