[gmx-users] Frozen atoms and energy group exclusion

toma0052 toma0052 at umn.edu
Mon Mar 5 19:32:00 CET 2007

     I asked a similar question to this a bit ago, but didn't get much of a
response.  I have a lipid bilayer system of 128 DPPC molecules in water.  I
want to fix the bottom face of the bilayer, and I am doing so by freezing the
positions of the first 12 atoms of the DPPC molecule.  The manual says that
with frozen groups, one should use energy group exclusions to avoid odd force
contributions. So, in my .mdp file, I define one energy group as froz (The
first 12 atoms of the DPPC molecules on the bottom face), and another as
not_excl (Everything that is not froz).  Then, I use:  energygrp_excl   =  
froz froz froz not_excl
to exclude the interaction of the frozen atoms with themselves and the
interaction between the frozen atoms and the rest of the system.
     When I run this through grompp, I get the following error:
WARNING 1 [file "dppc.top", line 19]:
  Can not exclude the lattice Coulomb energy between energy groups
Checking consistency between energy and charge groups...
Program grompp, VERSION 3.3
Source code file: grompp.c, line: 307

Fatal error:
atoms 3212 and 3213 in charge group 2179 are in different energy groups

Am I doing this incorrectly?  Should I be excluding the interactions with the
frozen groups in another way?  My dppc.top file, of which line 19 is the end,
looks as follows:

; topology for a pure DPPC bilayer with 128 lipids and 3655 SPC water
; molecules
#include "ffgmx.itp"
#include "dppc.itp"

#ifdef FLEX_SPC
#include "flexspc.itp"
#include "spc.itp"

[ system ]
; name
Pure DPPC bilayer with 128 lipids and 3655 water molecules

[ molecules ]
; name	number
DPPC    128
SOL     3655SOL

Thank you,
Mike Tomasini

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