<DIV>Hi dear gmx-users and developers,</DIV>
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<DIV>I'm working on a system involved with solid surface and solution, which using periodic boundary conditions in x and y directions only.<BR>I need to creat a virtual wall at both z=0 and z=z, but it should be a reflecting boundary conditions wall. <BR>It's like this: <BR>pretend that there is a virtual wall at z = z, when a water molecule (for example) is about to go though the wall, the wall plays like a mirror, reflecting the molecule's behavior beyond the wall back to the origin side, with the velocity component at Z direction changed to the opposite side.<BR>Is there a possible way to achieve this, and how? <BR>Should I change the code? and where is it?</DIV>
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<DIV>I tried the wall parameters based on wall_type, wall_atomtype, wall_density etc. with a pure water system, but there comes some problems. When it comes to the table.xvg, I have no exact idea about the parameter setting. The way I do is to copy the gmx_top_path/table6-12.xvg and make the coulomb interation and dispersion interaction zero, leaving the repulsive term's values unchanged. Then rename the table file to table_SOL_wall0.xvg and table_SOL_wall1.xvg separately.<BR>Some settings in .mdp are as below:<BR>nwall = 2<BR>wall_atomtype =SI SI<BR>wall_type = table<BR>wall_r_linpot = 2<BR>wall_density = 2000 2000<BR>wall_ewald_zfac = 3</DIV>
<DIV>I make the wall_density especially large, still some water come out of the box in z direction.</DIV>
<DIV><BR>I think the parameters setting and table.xvg is a little bit complicative for me. <BR>So, I do hope there is some way to use the reflecting boundary conditions wall, which doesn't need the parameters above.<BR>I need some hints badly and sincerely. Anyone can help me? Thank you!!</DIV>
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<DIV>Sincerely,</DIV>
<DIV>Kiara</DIV><br><br><span title="neteasefooter"><span id="netease_mail_footer"></span></span>