From: Peterson J (peterson.jjjj_at_gmail.com)
Date: Fri Jun 14 2013 - 15:44:46 CDT
Thanks for your list of possible problems that might cause the lipid
bilayer tear apart. I'm using the latest CHARMM, neutralized the system and
allowed ions to equilibrate. I have chosen NVT to keep the volume constant
so that I can avoid volume changes during the simulation. I will try NPT on
this system and check the system.
On Fri, Jun 14, 2013 at 3:34 PM, Aron Broom <broomsday_at_gmail.com> wrote:
> 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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