Dear all,<br><br>I'm trying to simulate with pbc=xy and I need two walls. My settings are as follows:<br><br>pbc = xy<br>nwall = 2<br>wall_atomtype = C C<br>wall_type = 9-3<br>
wall_r_linpot = -1 -1<br>wall_density = 20 20<br>wall_ewald_zfac = 3<br><br>The problem is how to define wall_atomtype in my topology file (top/itp)? A want to have this solid carbon wall with 9-3 potential. Where in my top/itp file can I define such atoms? This is my top file:<br clear="all">
<br>#include "ffG53a6.itp"<br>#include "spc.itp"<br><br>[ system ]<br>Pure Water with walls<br><br>[ molecules ]<br>SOL 216<br><br>When I gmxdump the generated tpr file, I saw no C atoms are defined; and it showed:<br>
<br> wall_atomtype[0] = 2<br> wall_atomtype[1] = 2<br><br>which corresponds to the hydrogen atom in my top file. And according to my forcefield, the LJ parameters for H is 0,0. So there is basically no wall. When I tried to simulate with this setting, the water molecules went out of the box (in z direction) and moved far away. And according to g_energy, there is no interaction energy between water and wall. So there indeed is no wall.<br>
<br>Can you help me with defining wall atom? If you have already finished any tasks with this wall algorithm, can you kindly attach your topology files to me?<br><br>Soooooooooooooooooo many thanks!!!!!!!!!!!!!!!!!<br><br>
<br>-- <br>Huaichen(Bobby) ZHANG<br><br>+31 648478172<br><div>MSc Sustainable Energy Engineering</div><div>Royal Institute of Technology (Sweden)<br></div><div>Eindhoven University of Technology (Netherland)</div><br>