CHARMM-GUI Polymer Builder for Modeling and Simulation of Synthetic Polymers

Abstract

Molecular modeling and simulations are invaluable tools for polymer science and engineering, which predict physicochemical properties of polymers and provide molecular-level insight into the underlying mechanisms. However, building realistic polymer systems is challenging and requires considerable experience because of great variations in structures as well as length and time scales. This work describes Polymer Builder in CHARMM-GUI (), a web-based infrastructure that provides a generalized and automated process to build a relaxed polymer system. Polymer Builder not only provides versatile modeling methods to build complex polymer structures, but also generates realistic polymer melt and solution systems through the built-in coarse-grained model and all-atom replacement. The coarse-grained model parametrization is generalized and extensively validated with various experimental data and all-atom simulations. In addition, the capability of Polymer Builder for generating relaxed polymer systems is demonstrated by density calculations of 34 homopolymer melt systems, characteristic ratio calculations of 170 homopolymer melt systems, a morphology diagram of poly­(styrene-b-methyl methacrylate) block copolymers, and self-assembly behavior of amphiphilic poly­(ethylene oxide-b-ethylethane) block copolymers in water. We hope that Polymer Builder is useful to carry out innovative and novel polymer modeling and simulation research to acquire insight into structures, dynamics, and underlying mechanisms of complex polymer-containing systems.

Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials

“…Starting coordinates for systems are built using a generic multiscale approach, in which first a super CG resolution representation of the system is generated, followed by a back transformation to the target level. This multiscale approach is similar to the procedure underlying the Charmm-GUI polymer builder 30 , but our approach is generic meaning parameters of the super CG model are derived on the fly based on the target force-field, employs a self-excluding random-walk in contrast to a full-scale dynamics simulation, and uses an automated back transformation, which does not rely on a library of coordinate fragments. The system-building proceeds in five steps (cf.…”

“…To our knowledge, there are no programs that can generate both input parameters and coordinates for arbitrarily complex polymeric systems independent of the force-field and compatible with HT approaches. Depending on the molecule or system there are a number of specific solutions 20 , 27 – 30 . Some of those are in principle capable of generating parameters and coordinates 29 , 30 .…”

“…Depending on the molecule or system there are a number of specific solutions. 20,[27][28][29][30] Some of those are in principle capable of generating parameters and coordinates. 29,30 However, available programs typically support only one force-field and are limited to specific (mostly linear) polymers implemented by the developers.…”

“…20,[27][28][29][30] Some of those are in principle capable of generating parameters and coordinates. 29,30 However, available programs typically support only one force-field and are limited to specific (mostly linear) polymers implemented by the developers. Website implementations 28,30 have the added problem that performance relies on server-load and it involves human-time having to interface with the website.…”

CHARMM‐GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field

“…In the area of simulation system preparation, most commercially available software packages, such as MOE (Chemical Computing Group), Maestro (Schrödinger), and Discovery Studio (BIOVIA) include system preparation capabilities, while there are academic tools such as CHARMM‐GUI and MDWeb, 19 among others. In particular, CHARMM‐GUI (https://www.charmm-gui.org), developed in the Im laboratory with contributions from a number of other groups, allows for the preparation of highly heterogeneous biomolecular systems and is recently expanding into non‐traditional biological systems such as polymers and materials 20–26 …”