Hi Mark,<br>Please accept my apology for not putting a descriptive subject line.<br>My query is regarding the periodic boundary condition only. I read from email archives regarding implementing periodic boundary conditions in XY plane and not in Z direction and one can do that by increasing the size of box in z direction by 2-3 times and thus creating a vacuum boundary. However, in my case molecules are still moving to other side (i.e -Z) and interacting with the gold surface. But what I want is interaction only at the top surface not the opposite surface. <br><br>I guess now problem is lucid.<br>Please help me if anything can be done to have a system where molecules can interact only at the top surface of gold layer not the below surface.<br><br>Regards<br>Rohit<br><br><b><i>Mark Abraham <Mark.Abraham@anu.edu.au></i></b> wrote:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> rohit gole wrote:<br>>
Dear All,<br><br>Please use a descriptive subject line so that people can use that to <br>work out whether they might be able to help you.<br><br>> I am trying to simulate tetrahydrofuran molecules with 3 layer gold surface.<br>> However, I would like to constrain my system in Z direction. I have <br>> tried to do that by increasing the box size in z direction by 3 fold but <br>> I still found few molecules coming toward other side. Is there any other <br>> way to implement the boundary conditions only in XY plane? <br><br>I'm afraid I don't understand this description of what you're trying to <br>do. Please have a read of the manual sections on *restraints* (not <br>*constraints*).<br><br>> or to have a <br>> repulsive wall potential at some z?<br><br>That's not implemented.<br><br>> And is it possible to place the system at the z=0 plane instead of <br>> having it at the center of simulation box either by using editconf or <br>> some
other?<br><br>No, but you can use trjconv after the simulation to get various effects. <br>It's just a translation anyway....<br><br>Mark<br>_______________________________________________<br>gmx-users mailing list gmx-users@gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br></blockquote><br><p> 
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