[gmx-users] waters in ion channels

[Samik Bhattacharya]

--- On Fri, 3/7/09, Itamar Kass <itamar.kass at gmail.com> wrote:

From: Itamar Kass <itamar.kass at gmail.com>
Subject: Re: [gmx-users] waters in ion channels
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Friday, 3 July, 2009, 3:42 PM

Hi,

I would say that those are water molecule which enter from the bulk
water. This is normal and probably important for the physiological
function of the system.

Best,
Itamar

thank you a lot for the answar. one thing i would like to ask again that how can i be sure that those water molecules are not inside the  hydrophobic core? and if they are not how deleting them could affect the system?
thanks again....
Shamik







On Fri, Jul 3, 2009 at 8:08 PM, Samik Bhattacharya<samikbhat at yahoo.co.in> wrote:
> hi i'm simulating a ion channel protein in DPPC membrane. i'm following
> Justin's tutorial for that. and have completed upto the solvation step. but
> right after solvation, i found some water molecules in the channel. now i
> want to delete those molecules. in the tutorial it is advised tyo use the
> keepbyz script to do that.. but after using that i didn't find any  change
> in the structure. watres are still present in there. may be i am making some
> mistake in running the program or something like that!!! can anyone suggest
> any thing to solve the problem...thanking you all in advance.
>
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