GaMD in NAMD

GaMD in NAMD2.13+ 

GaMD has been fully supported in NAMD2.13+. NAMD can be downloaded at: http://www.ks.uiuc.edu/Research/namd/.

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: GaMD_NAMD.tar

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: http://www.ks.uiuc.edu/Research/namd/


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)


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◇ Last updated: Mon, July 18, 2022