Difference between revisions of "NAMD"

Latest revision as of 13:45, 19 August 2022

Description

NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR.

Required Modules

Modules documentation

Parallel

intel/2016.0.109
openmpi/1.10.2
fftw
namd/2.11-cuda

Parallel with CUDA Support

intel/2016.0.109
openmpi/1.10.2
fftw
cuda/8.0
namd/2.11-cuda

Citation

If you publish research that uses NAMD you may want to cite it as follows:

James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26:1781-1802, 2005. abstract, journal

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Numerical]]
+[[Category:Software]][[Category:Molecular Dynamics]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|NAMD}}
 |{{#vardefine:url|http://www.ks.uiuc.edu/Research/namd}}
 <!--CONFIGURATION: OPTIONAL (1=ON)-->
-|{{#vardefine:exe|}} <!--RUNNING -->
+|{{#vardefine:exe|1}} <!--RUNNING -->
 |{{#vardefine:conf|1}} <!--CONFIGS-->
 |{{#vardefine:pbs|}} <!--PBS SCRIPTS-->
@@ Line 16: / Line 16: @@
 <!--Description-->
 {{#if: {{#var: url}}|
-{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}ks.)
+{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
-Fastest Fourier Transform in the West, is a C library for computing the Discrete Fourier Transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. Developed at MIT, it is by far the fastest implementation of FFT algorithm (upheld by regular benchmar<!--Modules-->
+NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM,  and X-PLOR.
+<!--Modules-->
 ==Required Modules==
 [[Modules|Modules documentation]]
 ===Parallel===
-*intel
+*intel/2016.0.109
-*openmpi
+*openmpi/1.10.2
 *fftw
-*namd
+*namd/2.11-cuda
-===Parallel with CUDA===
+===Parallel with CUDA Support===
-*intel
+*intel/2016.0.109
-*openmpi
+*openmpi/1.10.2
 *fftw
-*cuda
+*cuda/8.0
-*namd
+*namd/2.11-cuda
-<!--Additional-->
-{{#if: {{#var: exe}}|==Additional Information==
+{{#if: {{#var: pbs}}|==PBS Script Examples==
-DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY
+See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script example.|}}
+<!--Citation-->
+{{#if: {{#var: citation}}|==Citation==
+If you publish research that uses {{#var:app}} you may want to cite it as follows:<br/><br/>
+James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26:1781-1802, 2005. abstract, journal
 |}}
 <!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
 __NOTOC____NOEDITSECTION__