Example to run MD for molecular system

[xingyu-alfred-liu]

Hi Hoomd community,

I am very new to molecular dynamics and Hoomd, apologies in advance if my questions are naive. My background is mostly in DFT.

I want to run standard molecular dynamics for a molecular system (e.g. a box filled with benzene molecules). I tried to follow the tutorial here. And I encountered a few questions/issues, would like to get some help here. Thanks in advance!

1. In this tutorial, I noticed that the atom type is defined as a symbolic "A". I wonder if there is an easy way to define a realistic molecular system, such as Benzene (C and H instead of "A"), to easily place in the atomic mass, charge, coordinates etc into the gsd frame?
2. It's suggested to use MoSDeF suite, especially mBuild and foyer to build the system, and apply force field, respectively. However, there are a few things outdated here. This tutorial explained how to construct your simulation box, applying LJ potential, and convert that into a Hoomd format (GSD). However, these handy functions (mbuild.formats.hoomd_forcefield. create_hoomd_forcefield, mbuild.formats.gsdwriter.write_gsd) are not supported anymore in the latest mBuild release (v1.1). I tried to downgrade to v0.17 and those functions exist, but seems only support earlier version Hoomd (v2, v3).
3. I wonder if there is any packages/program can easily apply force field to atomic systems besides foyer. I only need interatomic force field, e.g. COMPASS. I tried foyer but there are lots of technical issues preventing it from working.

In summary, I only need to run a standard MD for a box of molecules, with classical forcefield enabled. A updated tutorial or suggestion to other programs is much appreciated!

[chrisjonesBSU]

Hi @xingyu-alfred-liu. Those mosdef/mbuild tutorials are a bit out of date! I did leave an example on the issue posted in mBuild.

[xingyu-alfred-liu]

Hi @chrisjonesBSU , thanks a lot! Will take a look at the other issue in mBuild

[joaander]

I will let the mBuild developers answer any questions related to those tools.

The 'A' in that tutorial is a generic example. You should replace it with an atomtype name used in your force field, and add all parameters for all types (and symmetric pairs of types). I default to names like 'A' and 'B' because those are the type names often used in coarse-grained bead-spring polymer simulations.

You will find in general that most features of HOOMD-blue are geared toward coarse-grained simulations. Specifically, HOOMD-blue provides a flexible API that allows you to build and customize your model. It interoperates with tools like mBuild and Foyer to enable atomistic simulations with similar goals. Check out other codes if you want a black box solution with a focus on atomistic simulations.

[xingyu-alfred-liu]

Thanks for the explanation! Will try other tools instead