From: Peterson J (peterson.jjjj_at_gmail.com)
Date: Fri Jun 14 2013 - 15:44:46 CDT
Hi Aron,
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.
-Peterson
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?
>
> ~Aron
>
>
> 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?
>>
>> Thanks,
>>
>> Peterson
>>
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
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