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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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