What about electrostatics? Ewald summation is probably the culprit here.
On Oct 24, 2014 12:05 PM, "Ramon Reigada" wrote:
> Hi,
>
> I would like to post a question about simulating with "Walls" in gromacs
> and using the Martini force field.
> The question is very simple. I am trying to simulate a simple box of water
> molecules with pbc=xy and walls at z=0 and z=z_box. I use Berendsen
> T-coupling and no pressure bath.
> I am trying:
>
> pbc=xy
> nwall =2
> wall_atomtype = C1 C1 (C1 are the alkane carbons defined in the martini
> force field file)
> wall_type = 9-3
> wall_density = 110 110
> wall_r_linpot = 1
>
> and all what I have is that the initial box of water molecules breaks in
> two
> pieces that separate each other in the z-direction.
> The same result (or a segmentation fault) is obtained by using 10-4 o 12-6
> LJ potentials, large wall_r_linpot values, other values of wall_densities,
> so I think that the problem is with the wall_atomtype. I tried the water
> bead (W) instead, and segmentation fault is obtained.
>
>
> thank you very much in advance,
>
> Ramon
>
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