From: Aron Broom (broomsday_at_gmail.com)
Date: Fri Jun 14 2013 - 15:34:31 CDT
I haven't done much with lipids, but I when I did they were pretty stable.
Two things to consider:
1) Is there a particular reason to use NVT versus NPT? Your bilayer may be
tearing apart because of incorrect pressures. On that note, which
forcefield are you using? Some lipid forcefields need you to use a
constant surface tension adjustment in order to be stable. I think the
latest CHARMM ones are OK, but certainly the older ones, and AMBER ones
still need that.
2) Have you neutralized the charge in the system and did you give the ions
time to equilibrate to their preferred positions near the headgroups?
On Fri, Jun 14, 2013 at 4:14 PM, Peterson J <peterson.jjjj_at_gmail.com> wrote:
> Hi all,
> I am currently simulating a membrane protein homology model embedded in
> lipid bilayer and performed simulated annealing and lipid melting steps
> successfully. But when the system is subjected under equilibration
> simulation (NVT) with constraints only on protein Ca atoms, I see the lipid
> bilayer tearing apart.
> What are the possible solution to solve this?
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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