Re: Re: How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system?

From: 张勇 (clarkzhy_at_mail.bnu.edu.cn)
Date: Thu Aug 25 2011 - 02:26:50 CDT

Thank you for your response. I do find the typical area per lipid and thickness for the lipid bilayer.

But what I really want to know is how to calculate area per lipid and thickness of the lipid bilayer in the every snapshot of MD trajectory obtained by NAMD. Is there some program or scripts to do with it?

 Clark Zhang

-----原始邮件-----
发件人: "Boyang Wang" <pkuwangboyang_at_gmail.com>
发送时间: 2011年8月25日 星期四
收件人: "张勇" <clarkzhy_at_mail.bnu.edu.cn>
抄送: namd-l_at_ks.uiuc.edu
主题: Re: namd-l: How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system?

Hi Yong,
 
in VMD, there is a lipid membrane builder, where you can find the typical area per lipid and thickness for the lipid bilayer. Maybe in the reference of you paper, you can cite the VMD reference.
 
Best,
Boyang

2011/8/25 张勇 <clarkzhy_at_mail.bnu.edu.cn>

Hi everyone,

Is there anyone here to know how to calculate the area per lipid and thickness for a lipid bilayer in a membrane-protein system?

Or, could anyone share the scripts to calculte them?

Any help will be highly appreciated!! Thanks in advance!

Clark

-- 
Boyang Wang, Ph.D.

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