[gmx-users] Error in lipid_protein simulation ( Energy minimization)

shabana yasmeen shabana.yasmeen90 at gmail.com
Mon Jul 13 06:42:39 CEST 2015

Dear Users!
 I am doing simulation of protein and lipids but facing problem in
energy minimization as I run:
grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o em.tpr
 i received Warnings as:
WARNING 1 [file ffnonbonded.itp, line 3098]:
  Overriding LJ-14 parameters.

WARNING 2 [file minim.mdp]:
  The sum of the two largest charge group radii (8.718670) is larger than
  rlist (1.300000)

I don't understand how to resolve these warnings.. If I ignore them
then at next step (mdrun -v -deffnm em) I get fatal error as:
Fatal error:
There is no domain decomposition for 12 nodes that is compatible with
the given box and a minimum cell size of 8.61095 nm
Change the number of nodes or mdrun option -rdd

If I do energy minimization using any other command as (mdrun -nt 1)
then I don't get EM.GRO file in the output.. Please help me to resolve
this issue..



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