[gmx-users] charges in vaccum simulations

pratibha kapoorpratibha7 at gmail.com
Sat Feb 15 08:39:04 CET 2014

Hello all

I have a small query regarding neutralization of charges in vaccum
I would like to simulate in vaccum 10 copies of 10 residue peptide
containing one charged residue lysine (I am interested in monitoring
cation-pi interactions between them). 

1) Would you suggest me to neutralize the system (since electrostatic
neutrality is required for the MD simulations of the system) even though I
would like to monitor cation pi interactions? 

2) How can I deal with the charges in-vaccum simulations? Since there are no
solvent molecules with dipole, would the addition of salt ions be
energetically be stable?

3)Also, I have read few papers in which MD simulations were carried out
without neutralization of charges. Is it reasonable to carry out such

Thanks in advance. 

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