Re: use of charmm27 & NPT ensemble for lipid bilayer simulation

From: Ruchi Sachdeva (ruchi.namd_at_gmail.com)
Date: Sun Jul 13 2008 - 23:09:57 CDT

Hi Liu,

It was a very small equilibration, just 500ps. Now I will try longer runs.
Thanks for your suggestions.

Ruchi

On 7/11/08, bo liu <liubo.njuer_at_gmail.com> wrote:
>
> Hi Ruchi,
> 2008/7/11 Ruchi Sachdeva <ruchi.namd_at_gmail.com>:
>
>> Dear all,
>>
>> I am new to lipid bialyer simulations and facing the following problem. I
>> have equilibrated my system containing a membrane protein embedded in POPC
>> bilayer using charmm27 & NPT ensemble on a linux cluster. I found that lipid
>> tails are overlapping with each other & thus bilayer thickness is getting
>> reduced throughout the simulation.
>
>
> i have also spotted the similar problem while dealing with DMPC (72
> lipids); The membrane seems to be squeezed at the beginning, however, after
> over 2ns MD run, the membrane gets back to normal! How long did you
> equilibrate the system?
>
> in my opinion, even if you have got one pre-equilibrated PDB file, it does
> not guarantee that you don't need to equilibrate the system before
> production run, unless you have also got the .vel file and do a
> restart-simulation.
>
>>
>>
>> Then I found a few namd posts (link1<http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/6863.html>,
>> link2<http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/6393.html>)
>> mentioning that use of charmm27 & NPT does not give correct lipid bilayer
>> parameters such as area per lipid (by Jensen et al., 2004<http://www.biophysj.org/cgi/content/abstract/86/6/3556>)
>> The parameters deviate from the experimental values. Instead one should
>> initially equilibrate holding the lipid head groups z coordinates in NPT
>> ensemble. Once area per lipid is set, then use constant area ie. NPzAT
>> ensemble. Or one can use NPgammaT simulation also.
>
>
> I think charmm27 is fine for lipids simulation if you have properly treated
> your system.
>
>
>>
>> Despite this report by Jensen et al., I found papers still using charmm27
>> force field alongwith NPT ensemble, which is not recommended. Moreover,
>> nothing is mentioned about lipid parameters. Can anyone please shed some
>> light on this. Am I missing something?
>
>
> My suggestions:
> 1. equilibrate the system at least for 2ns.
> 2. add sufficient water to the simulation box, at least 20 water molecules
> per lipid. if you use periodic boundary conditions, you have to make sure
> that the membrane and its image are seperated by bulk water for an enough
> distance.
>
> Hope it helps
>
> Cheers!
>
>>
>>
>> Thanks and Regards
>>
>> Ruchi
>>
>>
>
>
> --
> -Liu bo
> -----------------------------------------------------------
> Computational Biochemistry&Biophysics, Nano-bio systems: MD method;
> College of Chemistry and Chemical Engineering, Graduate University of
> Chinese Academy of Sciences, Beijing P.R. China
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