# TRD-NAMD

> **NIH NIH P41** · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · 2021 · $683,327

## Abstract

Project Summary / Abstract
The Center will continue the development of NAMD, a parallel molecular dynamics code for high-performance
simulation of large biomolecular systems. NAMD supports mainstream biomedical research into the dynamics of
cellular processes at atomic and sub-nanosecond resolution not achievable by experimental methods, and is used
typically hand-in-hand with cryo-electron microscopy imaging and other experimental techniques. The largest
NAMD simulations currently encompass entire viruses and cellular organelles.
 NAMD supports classical molecular dynamics simulations, most commonly of all-atom models with explicit sol-
vent and periodic boundary conditions with PME full electrostatics in an NPT ensemble, although coarse-grained
models, implicit solvent, and non-periodic or semi-periodic boundary conditions are also supported. CHARMM
and similar force fields are supported, including the Drude polarizability model. Built on this foundation are a
variety of features for steering simulations, including the ability to define collective variables as control parameters
for restraints or conformational free energy calculations. Also supported are alchemical free energy calculations and
methods for accelerating sampling, including user-customizable multiple-copy algorithms for parallel tempering
and conformational or alchemical free energy calculations.
 NAMD employs the prioritized message-driven execution capabilities of the Charm++/Converse parallel run-
time system enabling excellent parallel scaling on both Cray and IBM supercomputers and commodity workstation
clusters. NAMD is distributed free of charge as both source code and convenient precompiled binaries for Windows,
Mac OS X, and Linux, and supports both NVIDIA GPUs and Intel Xeon Phi coprocessors.
 The performance of NAMD simulations will be improved by optimizations for current and future generations of
GPUs such as NVIDIA Pascal and Volta, as well as the increasingly high core counts and wide vector instructions
of CPUs such as Intel Xeon and Xeon Phi. NAMD will be ported and tuned on pre-exascale supercomputers
including the Xeon Phi-based Theta and Aurora at Argonne National Laboratory and the GPU-based Summit
at Oak Ridge National Laboratory, enabling up to multi-billion atom simulations of entire viruses and organelles,
and building towards simulations of entire minimal cells on exascale supercomputers planned for 2023.
 The accuracy of NAMD simulations will be improved by the implementation of explicit solvent constant pH
ensemble simulation and by combined quantum-classical simulation via a new interface to the quantum chemistry
programs ORCA and MOPAC. Statistical confidence in simulation results will be improved by enhanced sampling
methods, in particular advanced multi-copy algorithms including exchanges with coarse-grained representations,
milestoning, generalized simulated annealing, and automated reaction coordinate search. The development of
these and other metho...

## Key facts

- **NIH application ID:** 10163204
- **Project number:** 5P41GM104601-32
- **Recipient organization:** UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
- **Principal Investigator:** Klaus Schulten
- **Activity code:** P41 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $683,327
- **Award type:** 5
- **Project period:** 1997-08-01 → 2022-09-27

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10163204

## Citation

> US National Institutes of Health, RePORTER application 10163204, TRD-NAMD (5P41GM104601-32). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10163204. Licensed CC0.

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