[gmx-users] Peptide, lipid simulation

Justin Lemkul jalemkul at vt.edu
Thu Oct 1 18:08:16 CEST 2015

On 10/1/15 9:07 AM, badamkhatan togoldor wrote:
> 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 !

The error and note 4 are related to the Verlet scheme, so switching to 
"cutoff-scheme = group" is needed here.  For note 5, it's probably not that big 
a deal in this context, but don't try to run a simulation with a plain cutoff.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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