[gmx-users] Help: Anyone worked with "Wall"?
Peter C. Lai
pcl at uab.edu
Thu Apr 5 22:29:21 CEST 2012
For walls, the atoms in the wall are virtual.
Remember that 9-3 LJ integratees over the volume behind the wall so you will
have to set your atom density appropriately. Setting wall_density to 20/nm^3
for 9-3 wall leads to 20 carbon atoms per nm^3. That's not going to be
totally solid, imo.
I am using 10-4 "2-D" walls to effect here:
nwall = 2
wall_type = 10-4
wall_density = 5 5
wall_atomtype = CG331 CG331
wall_r_linpot = -1
wall_ewald_zfac = 3
(CG331 is just a methyl group carbon specific to my forcefield).
On 2012-04-05 10:08:02PM +0200, Huaichen(Bobby) Zhang wrote:
> Dear all,
> I'm trying to simulate with pbc=xy and I need two walls. My settings are as
> 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
> wall_atomtype = 2
> wall_atomtype = 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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Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
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