Re: headgroup area calculation

From: ipsita basu (ibasu788_at_gmail.com)
Date: Wed Jul 14 2010 - 02:05:22 CDT

Thank you very much. But I couldn't match the headgroup area. That's
why I want to use NγPT simulation to reduce the headgroup area. How
can I introduce this in my configuration script as I am doing NPT
simulation. I have protein in my system, Will the introduction of NγPT
affect the protein structure? Please help.

On 7/12/10, Branko <bdrakuli_at_chem.bg.ac.rs> wrote:
>
> Hi Ipsita,
>
> Try with VegaZZ
> (http://nova.colombo58.unimi.it/cms/index.php?Software_projects:VEGA_ZZ:Download#Other),
> there you have option to calculate area of, by some criterion, selected
> atoms for the whole trajectory.
>
> Sincerely
>
> Branko
>
> On 7/12/2010 2:33 PM, ipsita basu wrote:
> Hi all,
> I want to calulate the headgroup area of DMPC lipid in dmpc
> bilayer which is running in namd, that's why dcd from namd is read in
> charmm script, but I found a very large value than the reported one. I
> download the initial bilayer from charmm-gui and found the same large
> value.
> Can you please tell me how can I get the correct value and any
> analysis method from where I can properly analyse the lipid headgroup
> area.
> Thank you very much.
>
>
>
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-- 
Ipsita Basu
Research Fellow
c/o : Dr. Chaitali Mukhopadhyay
Rajabazar Science College
92 APC Road
Kolkata - 700009

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