VMD-L Mailing List

From: nicolas martin (nicolasmartin973_at_gmail.com)
Date: Thu Mar 19 2015 - 09:29:20 CDT

Dear Joshua,

Thank a lot for your fast answer and the very interesting paper on SGLTs. I
will give a look at g_count and g_flux which seem to be very powerful and
come back to you if I'm having troubles.

Thanks a lot,

NM

2015-03-19 14:29 GMT+01:00 Adelman, Joshua Lev <jla65_at_pitt.edu>:

> Hi Nicolas,
>
> I'm still a little unclear about your counting method for the
> description you provided, but I think you might want to be a little
> careful. You can't really get accurate transitions from just looking at
> frames n and n - 1 in isolation. It is more typical to look at the entire
> history of each water molecule and split your simulation box into 3
> sections using 2 planes (lower bulk, channel, upper bulk). You only want to
> count transitions that go from the upper bulk to the lower bulk (or lower
> to upper), that go through the channel. It's not sufficient to look only at
> the crossings between pairs of regions, due to either periodic boundary
> crossings or movement between the channel and bulk that don't represent
> full transitions. We and others have used this method to look at permeation
> counts of waters and other molecules through channels and pores. An example
> of a detailed description of this is found in:
>
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3984995/
>
> and there is a discussion of the errors involved in the calculation due
> to finite time resolution in the trajectory in the supporting materials.
>
> While it's possible to do this using TCL scripting, I have always
> preferred to do this analysis outside of VMD, using a combination of Python
> and low-level c code. I can make this available to you, but I haven't had
> the time to package it in a clean way.
>
> There is also a gromacs tool that you might be able to use by Oliver
> Beckstein that already has this method coded:
> https://github.com/orbeckst/g_count
>
> Best wishes,
> Josh
>
>
>
>
>
> On Mar 19, 2015, at 4:04 AM, nicolas martin wrote:
>
> Dear all,
>
> I come to you with a problem which is as much related to scripting than
> it is to chemistry.
>
> I'm have a long trajectory of a protein channel in explicit solvent.
> Since I'm watching the transitions from opened to closed configuration of
> this channel I'd like to measure the quantity of water going through along
> time.
>
> I've figured out that counting the number of molecules that are up to the
> constriction point at frame n-1 and down to this constriction point at
> frame n or the other way around would give me the answer. But it's
> impossible (and pretty useless) to do for the water molecules of the whole
> system. so I came up with the idea to consider waters inside the channel
> only.
>
> It sounds really complicated to me to create an array which would contain
> the idea and z coordinated or the waters selected at frame n-1 and frame n
> so I can compare and see if a transition happens.
>
> So here are my questions. Are you aware of a script which could do that
> for me? Do you think my approach is meaningful ? Do you think there are
> better/faster/easier way to do it?
>
> Thanks a lot for your help,
>
> NM
>
> --
> Nicolas Martin
> PhD candidate at ISIS
> 67000 Strasbourg
> 06.29.73.12.73
>
>
>
>
> 

-- 
Nicolas Martin
PhD candidate at ISIS
67000 Strasbourg
06.29.73.12.73