Hi S. Xavier,

I don't understand exactly what you are asking?

Perhaps if you gave some details of the system you are trying to simulate, someone could point you in the right direction.

In MD simulations, you usually have to define the size of each atom (by molecule files or through the main script). The smallest size assigned to the atoms determines the scale of the model. Also the size of the time-step is really important.

Dear S. Xavier

If you are working with LAMMPS and your sample is metallic crystal in nanoscale, your dimension is in Angstrom unit.

Following example code related to the silver's metal in the box sample of 40X40X40 angstrom:

# ------------------------ INITIALIZATION ----------------------------

units metal

dimension 3

boundary p p p

atom_style atomic

variable latparam equal 4.09

# ----------------------- ATOM DEFINITION ----------------------------

lattice fcc ${latparam}

region box prism 0 40 0 40 0 40 0.0 0.0 0.0 units box

create_box 1 box

create_atoms 1 box

Hi Philip Kitchen , Peyman Aminpour , Navid Khademabbasi

Thank you very much for the response.

I want to compare the interactions of an organic molecule with water at ordinary and nano dimensions using gromacs software. How do we specify the size in nano dimension in gromacs and then proceed with NVT, NPT equilibrations? Could you please tell me? Thank you.

I don't understand what you mean by nano vs ordinary dimensions. The 'size' of your atoms (i.e. van der waals radius) is set by the forcefield you use and will correspond to experimentally determined values, or at least slightly tweaked experimental values that give the correct behaviour of some system (e.g. freezing points, partition coefficients, etc), and is independent of the size of the simulated system.

Do you mean that you want to compare the behaviour of your molecule in bulk water vs. behaviour in contact with only a small number of water molecules in vacuum?

Perhaps you could draw a sketch of the two systems you want to simulate? That might help us to understand what you're trying to do!

Philip Kitchen For example (1) urea and water interaction

(2) nanoparticle urea and water interaction

How to build the topology file accordingly?

Okay - so the question is how does my nanoparticle affect urea-water interactions?

Practically, to build the topology, the simplest way (for me anyway) is to have your nanoparticle parameters in a .itp file, then build your topology with something like:

#include "FORCEFIELD NAME.ff/forcefield.itp"

#include "nanoparticle.itp"

#include "urea.itp"

#include "tip3p.itp" (or whatever water model is appropriate)

[ system ]

Nanoparticle and urea in water

[ molecules ]

Nanoparticle X

Urea Y

SOL Z

Chapter 5 of the Gromacs manual has very detailed instructions on how to build topologies.

http://manual.gromacs.org/documentation/2018.3/manual-2018.3.pdf