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
electrostatics
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,
Felipe
+-----------------------------------+
| Luis Felipe Pineda De Castro, PhD |
| Computational Chemist - Postdoc |
| Linnaeus University |
| SE-391 82 Kalmar |
| Sweden - Sverige |
+-----------------------------------+
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
