[gmx-users] Peptide, lipid simulation

badamkhatan togoldor bdmkhtn at yahoo.com
Thu Oct 1 15:21:33 CEST 2015

Dear Gromacs Users,I would like to use g_membed to insert my peptide into membrane. But I got this errors and notes in grompp
ERROR 1 [file membed.mdp]:
  Energy group exclusions are not (yet) implemented for the Verlet scheme

NOTE 4 [file membed.mdp]:
  NVE simulation with an initial temperature of zero: will use a Verlet
  buffer of 10%. Check your energy drift!

NOTE 5 [file membed.mdp]:
  You are using a plain Coulomb cut-off, which might produce artifacts.
  You might want to consider using PME electrostatics.membed.mdp file include following options: integrator          = md
energygrps        = Protein
freezegrps         = protein
freezedim          = Y Y Y
energygrp_excl   = protein protein
nsteps               = 1000
So I don't know I have to put more options? or use other .mdp file? If someone have appropriate .mdp file, please share !    
 Badamkhatan Tuguldur

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