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

[Alan Dodd]

How about you try the different options, see what they do, and then decide for yourself how best to utilise them for whatever it is that you wish to do?



----- Original Message ----
From: ANINDITA GAYEN <aninditagayen at yahoo.co.in>
To: gmx-users at gromacs.org
Sent: Monday, May 19, 2008 2:28:30 PM
Subject: [gmx-users] Re: Re: water distortion above bilayer



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 <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] water distortion above bilayer
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <48311ADC.2040008 at anu.edu.au>
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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