[gmx-users] waters in ion channels
samikbhat at yahoo.co.in
Fri Jul 3 12:36:34 CEST 2009
--- 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
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.
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?
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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