[gmx-users] energy group exlusions for frozen structures-use of maxwarn -1?

Jennifer Williams Jennifer.Williams at ed.ac.uk
Thu Oct 28 11:57:36 CEST 2010


I am using a porous structure (MOF). I am interested in how guest  
molecules inside the porous structure interact with each other and the  
pores of the structure. As my structure represents a rigid crystalline  
framework it is usually kept rigid/frozen and only non bonded  
parameters (LJ and electrostatics) are taken into account for this  

(I think) I read somewhere on the forum the energy group exclusions  
should be applied for frozen atoms (also if I don?t do this I get some  
v. large energies).

So I use the following in my .mdp file

; Selection of energy groups
energygrps               = MOF

; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl           = MOF MOF

However on running grompp I get the following warning:

WARNING 1 [file MCM_TDI.top, line 32874]:
   Can not exclude the lattice Coulomb energy between energy groups

Why is this? My frozen structure has partial charges but is overall  
charge neutral.
To get around this I have to use maxwarn -1. I am a bit wary of using  
maxwarn. Can someone advise whether it is sensible to use maxwarn in  
this case?



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