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

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 23 17:12:00 CET 2010

Matthew Watkins wrote:
> 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.

I don't mean to hijack the thread, but this sort of thing would make an 
excellent "How-To" on the Gromacs wiki site, if you have time to contribute it. 
  Tabulated potentials seem to frustrate many users.  Although there are a 
number of threads in the list archive with excellent information, it would be 
great to have a wiki page for it all instead of piecing it together from 
(sometimes incomplete) posts.


> 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.
> Cheers,
> Matt
> 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


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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