[gmx-users] dielectric coffiecient

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 28 12:01:39 CET 2008

shahrbanoo karbalaee wrote:
> Deat justin
> thanks for your help.
> I delete cl- from (peptide,tfe ,water) in my system and I see about
> his charge not get message. when I add tfe in peptide (pdb2gmx -f
> name.pdb -ter -ignh )the lysin amino acid is protonated (2
> lysin).another charge aminoacid is D,E.do you think it related to
> adding tfe to system.because my peptide charge is +1.please advise me.
> and another ,do I need to define e (dielectric E) for water and tfe
> in my mdp files ?or has the program  default?

If your peptide has a net charge of +1, then you need a counterion to neutralize 
the charge.  But I'm confused.  If you have 2 Lys and an Asp and Glu, then the 
net charge should be 0, unless you've done something strange with your termini.

There is no need to set a dielectric, at least not with PME for electrostatics. 
  If you're using reaction field, then you would specify a dielectric beyond a 
certain cut-off.


> best


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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