[gmx-users] Peptide, lipid simulation
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 !
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