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Department of Pharmacology

GaMD-NAMD: Installation

GaMD in NAMD2.13+ 

GaMD has been fully supported in NAMD2.13+. Download NAMD from this webpage

GaMD patch for NAMD2.11 / NAMD2.12:

You can click the following link for a patch that adds temporay support to NAMD 2.11 / NAMD2.12 (zip file)

Installation

1. Replace the four NAMD2.11 source code files with those from the directory “./src_namd2.11”: “Controller.h”, “Controller.C”, “SimParameters.h” and “SimParameters.C”

2. Re-compile NAMD following the original instructions.

Precompiled GaMD-NAMD:

On XSEDE Comet:
/home/yin/namd_gamd-comet/namd_2.11-gamd/Linux-x86_64-icc/namd2

On XSEDE Gordon:
/home/yin/namd_gamd/namd_2.11-gamd/Linux-x86_64-icc/namd2

Reference

Pang, Y.T.#, Y. Miao#,*, Y. Wang* and J. A. McCammon* (2017) Gaussian accelerated molecular dynamics in NAMD, J Chemical Theory and Computation, 13(1): 9-19. (Abstract | PDF)