Hi Chris<br>Thank you for your suggestions!<br><br>These days I also tried anisotropic and semiisotropic for my simulation, but I still got the same result, so I wonder maybe there's something wrong with my initial structure, but it will take time to check it out.
<br><br>I'm trying to use the method you suggested, I searched the list, find there is some scripts offered by other users, but I'm new to Linux and gromacs, I've got no idea which one to use and how to use it. So would you please send me a sample?
<br><br>Thank you very much for your help<br><br>Xin Liu<br><br><div><span class="gmail_quote">On 9/5/06, <b class="gmail_sendername"><a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a></b> <<a href="mailto:chris.neale@utoronto.ca">
chris.neale@utoronto.ca</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">It is unclear why your second method works for you. However, given that it does,
<br>just use genbox -cs spc216.gro -cp 183_system_that_worked.gro -box 9.2 9.2 8.3<br>and then use your own script to remove any spc waters that were put inside the<br>membrane and modify the nubers in your topology file accordingly.
<br><br>I imagine that your first attempt didn't work since an entire dppc molecule is<br>removed upon a single collision and this will lead to "holes" in your membrane<br>that will quickly fill with water. Of course this should also have happened in
<br>your second attempt... I am not sure what was different there.<br><br>You need semiisotropic pressure coupling and you need to stop every once and a<br>while and remove any water molecules that are inside the membrane. Note that
<br>isotropic Pcoupling in a membrane system (as you have been doing) has the<br>potential to provide a surface tension (or the opposite) that you have not been<br>intentionally including and so you can expect your membrane to behave differently.
<br><br>Chris.<br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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