[gmx-developers] Implementing a new type of VdW interaction

Mark Abraham mark.abraham at anu.edu.au
Thu May 5 08:01:44 CEST 2011

On 05/05/11, Lee-Ping  <leeping at MIT.EDU> wrote:
> Dear all,
> I would like to implement a new type of vdW interaction.  It's similar
> to the Buckingham interaction, so I was thinking of adding the
> interaction in nb_generic.c with ivdw set to 4.  

First, test the idea with the nonbonded interaction tables - see manual and webpage. Don't get hands dirty unnecessarily

> ivdw will be set to four when the Buckingham interaction is turned on
> with the combination rule set to 2 (currently this is unused).
> Unfortunately, it seems like the integer corresponding to the
> combination rule (comb) is used only in grompp, and when we get to mdrun
> it is lost.  
> For LJ parameters, I understand why this makes sense; because grompp
> does all the parameter processing, and the nonbonded kernels always see
> c6 and c12 and then apply the same formula; they don't care about the
> user input because grompp takes care of all that.

Right, but grompp records them together with their type. Check out gmxdump on a .tpr
and compare with stuff in src/gmxlib/ifunc.c

> Since my interaction function actually uses a different functional form,
> I can't simply combine the parameters differently in grompp and pass
> them into the Buckingham kernel.  I need a switch in the forcerecord
> that decides between whether to call the normal Buckingham interaction
> or my custom one.

Use of Buckingham is triggered by mdrun noticing the types recorded in the .tpr, so you can do a similar thing.


> Is my analysis correct?  How do I pass the combination rule into "mdrun"
> so I can trigger my custom VdW interaction?
> (My current idea is to add the variable into the main gmx_mtop_t
> topology.  Please let me know if there's a better idea.)
> Thank you,
> - Lee-Ping
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