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

[Mark Abraham]

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.

Mark


> 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
> 
> -- 
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-developers-request at gromacs.org.
> 
> 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20110505/65ceb4fa/attachment.html>