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 <[EMAIL PROTECTED]> To: [email protected] 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 <[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 ________________________________ Unlimited freedom, unlimited storage. Get it now
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