<table cellspacing='0' cellpadding='0' border='0' ><tr><td style='font: inherit;'><br>How to be sure that the water is moving from the leaflet to the
other leaflet? Can I see it from any analysis? How can i trace a water
that is moving due to pbc and how to originate a pdb that will show the
pdb that will be visually good for analysis (I am confused about the
-pbc nojump and -pbc whole comands). Please send suggestions.<br><br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><pre><br>Message: 5<br>Date: Mon, 19 May 2008 16:14:52 +1000<br>From: Mark Abraham <Mark.Abraham@anu.edu.au><br>Subject: Re: [gmx-users] water distortion above bilayer<br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>Message-ID: <48311ADC.2040008@anu.edu.au><br>Content-Type: text/plain; charset=UTF-8; format=flowed<br><br>ANINDITA GAYEN wrote:<br>> Hi all,<br>> <br>> In the TIP4P water layer above my dmpc bilayer after 100ps (OPLS-BERGER) <br>> a hole is being formed. Some water molecules are absent in the water <br>> layer, but the total no of water molecules are same. This is my semi.mdp <br>> file<br><br>This sounds like normal behaviour under periodic boundary conditions. <br>Check the other side of the boundaries. See
<br>http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions<br><br>Mark<br><br><br><br></pre></blockquote></td></tr></table><br>
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