[gmx-users] Problem with Lennard Jones cross terms

[Gaurav Goel]

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

> Dear Gaurav
>
> Thanks a lot for your quick reply
>
> I have done also what you suggested but the result is the same. I mean that
> I observe stronger adsorption of the polymers to the surface, when I
> increased the values of c6 and c12 for Si  in the [atomtypes], but
> continue having original values in the *[ nonbond_params ].*
> But in general, am I not able with gromacs to switch-off the LJ
> interactions between the polymers and the substrate?
> Is it possible to have this problems because I use NVT ensemble?
>

You can switch-off all non-bonded interactions between a pair of energy
groups by defining Energy group exclusions. Sec. 7.3.19 of the gromacs
manual 4.0.

-Gaurav

>
> Thanks again, Chrysostomos
> --- Στις *Πέμ., 01/07/10, ο/η Gaurav Goel <gauravgoeluta at gmail.com>*έγραψε:
>
>
> Από: Gaurav Goel <gauravgoeluta at gmail.com>
> Θέμα: Re: [gmx-users] Problem with Lennard Jones cross terms
> Προς: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Ημερομηνία: Πέμπτη, 1 Ιούλιος 2010, 16:10
>
>
> 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<http://mc/compose?to=cbatiss@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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