[gmx-users] Re: Re: water distortion above bilayer

Mon, 19 May 2008 06:29:06 -0700


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.


Message: 5
Date: Mon, 19 May 2008 16:14:52 +1000
From: Mark Abraham <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] water distortion above bilayer
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=UTF-8; format=flowed

ANINDITA GAYEN wrote:
> Hi all,
> 
> In the TIP4P water layer above my dmpc bilayer after 100ps (OPLS-BERGER) 
> a hole is being formed. Some water molecules are absent in the water 
> layer, but the total no of water molecules are same. This is my semi.mdp 
> file

This sounds like normal behaviour under periodic boundary conditions. 
Check the other side of the boundaries. See
 
http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions

Mark






      
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