--- On Fri, 3/7/09, Itamar Kass <[email protected]> wrote:
From: Itamar Kass <[email protected]>
Subject: Re: [gmx-users] waters in ion channels
To: "Discussion list for GROMACS users" <[email protected]>
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<[email protected]> 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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