From: nicolas martin (
Date: Thu Mar 19 2015 - 03:04:26 CDT

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

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,


Nicolas Martin
PhD candidate at ISIS
67000 Strasbourg