Dear all, I'm trying to simulate with pbc=xy and I need two walls. My settings are as follows:
pbc = xy nwall = 2 wall_atomtype = C C wall_type = 9-3 wall_r_linpot = -1 -1 wall_density = 20 20 wall_ewald_zfac = 3 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: #include "ffG53a6.itp" #include "spc.itp" [ system ] Pure Water with walls [ molecules ] SOL 216 When I gmxdump the generated tpr file, I saw no C atoms are defined; and it showed: wall_atomtype[0] = 2 wall_atomtype[1] = 2 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. 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? Soooooooooooooooooo many thanks!!!!!!!!!!!!!!!!! -- Huaichen(Bobby) ZHANG +31 648478172 MSc Sustainable Energy Engineering Royal Institute of Technology (Sweden) Eindhoven University of Technology (Netherland)
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