<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt">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?
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<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">----- Original Message ----<BR>From: ANINDITA GAYEN <aninditagayen@yahoo.co.in><BR>To: gmx-users@gromacs.org<BR>Sent: Monday, May 19, 2008 2:28:30 PM<BR>Subject: [gmx-users] Re: Re: water distortion above bilayer<BR><BR>
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<TD><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="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid"><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><A href="http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions" target=_blank>http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions</A><BR><BR>Mark<BR><BR><BR><BR></PRE></BLOCKQUOTE></TD></TR></TBODY></TABLE><BR>
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