[gmx-users] VMD Compatibility Question

[Alex]

Not really sure what simulations one can conduct in VMD, because it is 
primarily a visualization program. That aside, whether you can simulate 
systems containing non-biomolecular structures (metal nanoparticles, 
solid-state nanomaterials, etc) really depends on what physics you'd 
like to reveal. For things like nanomechanical properties, forcefields 
in Gromacs, NAMD, etc are only capable of reproducing zero Kelvin 
properties and it's a fundamental limitation. LAMMPS offers a far richer 
range of interaction potentials for those purposes, not just springy stuff.

In general, metal surfaces and their interactions with other things 
especially at the nanoscale cannot be accurately described by classical 
MD. It's a topic far beyond the scope of this board.

Alex


On 12/28/2017 11:55 PM, Ethan Hsiao wrote:
> Users Charlie and I want to perform MD simulations on transition metal
> nanoparticle interactions with different types of lipid rafts. Is it
> possible to conduct a simulation on VMD with a gold nanoparticle built from
> openMD with a lipid raft and cell membrane from GROMACS? Further, do you
> have any advice on how to do a metal nanoparticle simulation with cell
> membrane with GROMACS, NAMDm openMD, or whichever software your lab focuses
> on?
>
> Thank you,
> Ethan