<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><br><br>--- On <b>Fri, 3/7/09, Itamar Kass <i><itamar.kass@gmail.com></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Itamar Kass <itamar.kass@gmail.com><br>Subject: Re: [gmx-users] waters in ion channels<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Friday, 3 July, 2009, 3:42 PM<br><br><div class="plainMail">Hi,<br><br>I would say that those are water molecule which enter from the bulk<br>water. This is normal and probably important for the physiological<br>function of the system.<br><br>Best,<br>Itamar<br><br>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?<br>thanks again....<br>Shamik<br><br><br><br><br><br><br><br>On Fri, Jul 3, 2009 at 8:08 PM, Samik Bhattacharya<<a ymailto="mailto:samikbhat@yahoo.co.in" href="/mc/compose?to=samikbhat@yahoo.co.in">samikbhat@yahoo.co.in</a>> wrote:<br>> hi i'm simulating a ion channel protein in DPPC membrane. i'm following<br>> Justin's tutorial for that. and have completed upto the solvation step. but<br>> right after solvation, i found some water molecules in the channel. now i<br>> want to delete those molecules. in the tutorial it is advised tyo use the<br>> keepbyz script to do that.. but after using that i didn't find any change<br>> in the structure. watres are still present in there. may be i am making some<br>> mistake in running the program or something like that!!! can anyone suggest<br>> any thing to solve the problem...thanking you all in advance.<br>><br>> ________________________________<br>> Yahoo!
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