[gmx-users] Simulation of charged systems

Felipe Pineda, PhD luis.pinedadecastro at lnu.se
Thu Nov 1 11:17:52 CET 2012

Dear Colleagues,

I am currently carrying out MD simulations on models of archaeal 
membranes. These membranes, contrary to those of bacteria or eukariota, 
are made of unconventional lipids. In my case they contain a neutral 
carbohydrate headgroup and the second one is a negatively charged 
phospho-myoinositol, contrary to neutral (zwitterionic) phosphocholine 
found in conventional lipids. In order to have a neutral system to carry 
out the simulation on:

1. I could add 36 positive counterions (eg, Na+) to my membrane model, 
which would correspond to approx. 900 mM of these ions for the amount of 
water molecules I am using. This concentration is of course not only 
much higher than a physiological one, although it is, strictly speaking, 
not a salt, i.e. NaCl, concentration. The issue is that I would like to 
study the effect of salt (alkali cations) on the membrane properties and 
therefore would need a suitable, possible ion/salt-free system as 
reference state.

2. I could protonate the phosphate and have -O-P(OOH)-O- instead of 
-O-P(O2-)-O-. This would provide a neutral, salt-free reference state, 
but the issue is that this phosphate group would be probably 
de-protonated in the cellular compartment it is localized, which has a 
pH of approx 6.

Another option would be to run the simulations on the charged system, 
without counterions, but I am not quite sure if there are technical 
problems with that. I am using the following settings for the treatment 
of long-range electrostatics:

; Electrostatics
coulombtype     = PME           ; Particle Mesh Ewald for long-range 
pme_order        = 4                ; cubic interpolation
fourierspacing  = 0.16           ; grid spacing for FFT

I wonder if someone could kindly advise me in this issue.

Any suggestion or comment will be highly appreciated.

Best regards,


| Luis Felipe Pineda De Castro, PhD |
| Computational Chemist - Postdoc   |
| Linnaeus University               |
| SE-391 82 Kalmar                  |
| Sweden - Sverige                  |

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