Difference between revisions of "NAMD"
| (13 intermediate revisions by 4 users not shown) | |||
| Line 1: | Line 1: | ||
| − | [[Category:Software]][[Category: Molecular Dynamics] | + | [[Category:Software]][[Category:Molecular Dynamics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|NAMD}} | |{{#vardefine:app|NAMD}} | ||
|{{#vardefine:url|http://www.ks.uiuc.edu/Research/namd}} | |{{#vardefine:url|http://www.ks.uiuc.edu/Research/namd}} | ||
<!--CONFIGURATION: OPTIONAL (1=ON)--> | <!--CONFIGURATION: OPTIONAL (1=ON)--> | ||
| − | |{{#vardefine:exe|}} <!--RUNNING --> | + | |{{#vardefine:exe|1}} <!--RUNNING --> |
|{{#vardefine:conf|1}} <!--CONFIGS--> | |{{#vardefine:conf|1}} <!--CONFIGS--> | ||
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
| Line 23: | Line 23: | ||
[[Modules|Modules documentation]] | [[Modules|Modules documentation]] | ||
===Parallel=== | ===Parallel=== | ||
| − | *intel | + | *intel/2016.0.109 |
| − | *openmpi | + | *openmpi/1.10.2 |
*fftw | *fftw | ||
| − | *namd | + | *namd/2.11-cuda |
| − | ===Parallel with CUDA=== | + | ===Parallel with CUDA Support=== |
| − | *intel | + | *intel/2016.0.109 |
| − | *openmpi | + | *openmpi/1.10.2 |
*fftw | *fftw | ||
| − | *cuda | + | *cuda/8.0 |
| − | *namd | + | *namd/2.11-cuda |
| − | <!-- | + | |
| − | {{#if: {{#var: | + | {{#if: {{#var: pbs}}|==PBS Script Examples== |
| − | + | 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--> | <!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | ||
__NOTOC____NOEDITSECTION__ | __NOTOC____NOEDITSECTION__ | ||
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
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