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

From: Boyang Wang (pkuwangboyang_at_gmail.com)
Date: Thu Aug 25 2011 - 02:32:01 CDT

Hi Clark,

based on my experience, I don't know such a program or script. I seems that
there is not a clear standard of how to judge the boundary of a lipid and
lipid bilayer. I suggest you to write a program where you set your
definition, and this might be good for the readers of your research to
follow.

Best,
Boyang

On Thu, Aug 25, 2011 at 3:26 PM, 张勇 <clarkzhy_at_mail.bnu.edu.cn> wrote:

> 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.
>
>
>

-- 
Boyang Wang, Ph.D.

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