On Fri, Jul 5, 2013 at 8:20 PM, Manikanthan Bhavaraju <
manikanthanbhavaraju.gmail.com> wrote:
> Dear Amber developers,
>
> I have equilibrated and sampled a protein+lipid bilayer (POPC) system by
> maintaining 0.1 M KCl concentration for 80ns using explicit solvent model
> with Amber12 and ff99SB + lipid11 forcefields. The N-terminus (residues
> 1-19) of the protein is anchored into the lipid bilayer. I have reimaged
> the system using ptraj for every 10 ns. Upon inspecting the reimaged pdb
> file in the VMD, I have observed that the majority of the K+ and Cl- ions
> have formed crystals (in the form of FCC lattice). Starting from a few
> crystal (smaller in size), by the end of 80ns of simulation the K+ Cl- ions
> have aggregated to form a larger crystal. Is this a forcefield effect due
> to ff99SB or Lipid11?
>
Probably neither. It's probably due to the ion parameters you used, and I
didn't see that you mentioned which parameters you used. You should use
the monovalent ion parameters designed for the specific water model you are
using. For instance, if you are using TIP3P, you should put a command like
loadAmberParams frcmod.ionsjc_tip3p
or the equivalent one for TIP4Pew or SPCE. If you use the ff10 force field
(which is equivalent to ff99SB for proteins), then using these new
parameters for ions is enforced.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jul 05 2013 - 19:00:02 PDT
