Re: Ways to find water molecules passing through the water channel in lipid bilayer

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Jan 18 2018 - 18:54:48 CST

It's not entirely clear given the language, but if there is a specific
protein channel in the lipid bilayer (i.e. it's not just lipid) you could
always try wrapping only the Z dimension. Have a look at the pbctools code
for inspiration.

Giacomo

On Thu, Jan 18, 2018 at 7:43 PM, Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
wrote:

> Dear Mr. Giacomo,
>
> Thanks for your reply. I have used pbc unwrap to unwrap water. But my
> concern is how can I analyse results (may be dcd file) to find out water
> molecules passing through the channel.
>
>
> Rabeta Yeasmin
>
> On Thu, Jan 18, 2018 at 6:38 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Try using pbc unwrap and analyze the result?
>>
>> On Thu, Jan 18, 2018 at 7:19 PM, Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
>> wrote:
>>
>>> Dear NAMD users,
>>>
>>> I want to calculate water molecules that are crossing through the
>>> channel of a lipid bilayer. It is very difficult to track water molecules
>>> visually which are passing through the channel in VMD as there are a lot of
>>> water molecules. And also I am confused about the unwrapping the water
>>> molecules to calculate the velocity at which water is passing through the
>>> channel. Because I can track an water molecule passing through the channel
>>> visually but when I check the pdb file, some of its x, y coordinate are
>>> outer side of the simulation box (in unwrapped water molecule). So I wonder
>>> if they are outer side of the simulation box how they cross the channel
>>> through the lipid.
>>>
>>> I will be grateful if anyone can suggest me any way to calculate water
>>> molecules passing through lipid bilayer and their velocity/diffusion rate.
>>>
>>> Thanks.
>>>
>>> Rabeta Yeasmin
>>>
>>
>>
>>
>> --
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Contractor, National Institutes of Health, Bethesda, MD
>> http://goo.gl/Q3TBQU
>> https://github.com/giacomofiorin
>>
>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

This archive was generated by hypermail 2.1.6 : Sun Sep 22 2019 - 23:19:17 CDT