[gmx-users] Simple LJ system

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 5 14:08:52 CET 2012

Jeff Armstrong wrote:
> I have literally just started using gromacs and hopefully have a pretty 
> straight forward question. Firstly I am interested in simulating a 
> binary Lennard-jones system with arbitrary choices of parameters (i.e. I 
> may choose the epsilon and sigma). If someone could summarise what 
> ingredients I would need for this it would be greatly appreciated. My 
> current understanding of topology files and .itp files is fairly limited 
> so a comprehensive reply will be very much appreciated.

You can follow a similar force field structure like any of the ones that already 
exist in Gromacs, except that you don't need any bonded parameters.  You need a 
[defaults] directive to define interaction types, [atomtypes] to define the 
nonbonded parameters of your species, and then you can proceed to the 
[moleculetype] and [atoms] levels.  All of this can be done within a unified 
.top, or you can create your own custom force field that can be #included within 
other topologies, making your own forcefield.itp (to have the [defaults] and any 
necessary #include statements) and ffnonbonded.itp for the [atomtypes].



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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