[gmx-users] Problem with Lennard Jones cross terms

[Gaurav Goel]

By specifying both c6 and c12 to be zero, you've set both the attractive and
repulsive components of SI-OA, Si-CH2, Si-CH3 dispersion interactions to
zero. If you don't have any electrostatic repulsions in your system polymer
might be "attracted" to Silica substrate for entropic reasons...e.g.,
centers of  mass of Si and CH2 can overlap without any energy penalty.

One solution will be to fix c6, c12 for  SI-OA, Si-CH2, Si-CH3 to their
original values under *[ nonbond_params ] *and then do whatever you want to
do with the Si-Si interactions in [atomtypes].

-Gaurav

2010/7/1 xrysostomos sfhsdfghsdfhsdgh <cbatiss at yahoo.gr>

> I am trying to simulate the following system: 5-layer FCC substrate
> consisting of Si particles which interact only with Lennard-Jones potential
> and vertical to the substrate I put polymer chains of (CH2-OA), starting
> from a distance of 0,4nm.
>
> What I want is to be able to manage completely independently the LJ
> interactions between the substrate and the polymers and not according to the
> combination rules, i.e. to have very very strong LJ interaction only between
> the Si particles but these to interact normally with the polymer chains.
>
> I use the Gromos-96 force-field. The initial values for the c6 and c12
> parameters are the following:
>
> *[ atomtypes ]*
>
> name  at.num   mass      charge  ptype            c6
> c12
>
> OA          8          0.000      0.000     A         0.0022619536
> 1.505529e-06
>
> CH2        6          0.000      0.000     A         0.0074684164
> 3.3965584e-05
>
> SI            14        0.000      0.000     A         0.01473796
> 2.2193521e-05
>
>
>
> *[ nonbond_params ]*
>
> i           j      func          c6                       c12
>
> SI       OA      1      0.0000000      0.00000000
>
> SI      CH2     1      0.0000000      0.00000000
>
> SI      CH3     1      0.0000000      0.00000000
>
>
>
> What I did is to run 2 different simulations in NVT ensemble. In the *
> first*, I multiplied by 10 the c6, c12 values of Si in the [atomtypes ]  and
> in the *second* I multiplied (the initial values again) by 100. In both
> cases I didn’t change the values on the [nonbond_params ].
>
> I would expect that in both cases there should be no adsorption of the
> polymers in the substrate, since I  change the interaction between the
> substrate and the polymers in the [nonbond_params ] equal to zero.
>
> What I observed is that after 50000 steps with 2 fs time step the polymers
> in the second case adsorbed to the surface.
>
> Can anybody help me or explain me why is this happening?
>
>
>
> Thanks in advance
>
>
>
> Chrysostomos
>
>
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