[gmx-users] Using lennard jones and buckingham terms simultaneously

Matthew Watkins matthew.watkins at ucl.ac.uk
Tue Mar 23 16:39:15 CET 2010

Hi Gareth,

as Vitaly suggested tabulated potentials seem to be the only way to go, 
it took me a while to get up to speed on the Gromacs way of doing this, 
so get in touch if you wish.

The tables for buck potentials need to include the standard 1/r6 term 
whilst what would be the 1/r12 term needs to contain exp(-Bx.rho), the 
C6 and C12 coefficients can then be put in a standard nonbonded section. 
  You'll need a separated table for each pair of interactions that 
interact with buckingham potential.  Each pair must be an energy group 
as well.

If there is a simpler method I'd love to hear it.



Gareth Tribello wrote:
> Hello
> I would like to use gromacs-4 to do a simulation of a small protein in 
> water and in the presence of calcium carbonate.  The potential I have 
> for the calcium carbonate uses Buckingham terms for the interaction 
> between the calcium and carbonate ions, while the protein obviously 
> interacts through Lennard Jones terms.  It is my understanding from the 
> manual that it is not possible to mix these two interaction types and so 
> it is not possible to do this simulation.  Also when I attempted to mix 
> lennard jones and buckingham terms in a topol.top file grompp complained. 
> Is there anyway around this problem?   
> Many thanks
> Gareth

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