[gmx-users] Re: periodic_molecule & missing interactions

[Dr. Vitaly Chaban]

I think it is a dangerous practice to simulate with a cutoff of 0.5 nm.
Irrespectively of what you study.

Dr. Vitaly V. Chaban


On Fri, Aug 30, 2013 at 11:32 AM, Valentina <valentina.erastova at durham.ac.uk
> wrote:

> Thank you for your reply.
>
> My box is quite small indeed, so my cut-offs are 0.5
>
> If I make a single layer, I would have to run quite a small system in
> z-direction.
> My residue box size:    0.62840   0.54421   1.60000   0.00000   0.00000
> -0.31420   0.00000   0.00000   0.00000
>
> My suspect of the problem
> In my system I have Al, bonded to 6 OH, and Mg, that is non-bonded, so only
> LJ. My nrexcl is set to 2, as I don't have dihedrals. The Al and Mg form a
> mesh, that should be infinite in xy-
>
> I am guessing what I have to do is to artificially connect those Mg to OH
> with k=0 bonds & angles (?) and then include [ pairs ] of Mg O and Mg H to
> be calculated as LJ?
>
> I have a non usual FF, hence cannot figure out how to implement it yet.
>
> Thank you for help, V
>
>
>
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