Namd: Difference between revisions
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#REDIRECT[[NAMD]] |
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{| width=760px class="wikitable" |
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|- |
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! Description !! Content |
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|- |
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| module load |
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| chem/namd |
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|- |
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| Availability |
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| [[BwForCluster_JUSTUS_2]] |
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|- |
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| License |
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| Freeware for non-commercial use. [[#License|More...]] |
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|- |
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| Citing |
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| [http://www.ks.uiuc.edu/Research/namd/papers.html Publications] |
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|- |
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| Links |
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| [http://www.ks.uiuc.edu/Research/namd/ Homepage] | [http://www.ks.uiuc.edu/Research/namd/2.14/ug/ Documentation] |
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|- |
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| Graphical Interface |
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| No |
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|} |
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= Description = |
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'''NAMD''' (NAnoscale Molecular Dynamics) is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. |
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= Availability = |
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NAMD is available on selected bwHPC-Clusters. A complete list of versions currently installed on the bwHPC-Clusters can be obtained from the [https://www.bwhpc.de/software.html Cluster Information System (CIS)]. |
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In order to check which versions of NAMD are installed on the compute cluster, run the following command: |
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<pre> |
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$ module avail chem/namd |
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</pre> |
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= License = |
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NAMD is available as [https://en.wikipedia.org/wiki/Freeware freeware] for non-commercial use by individuals, academic institutions, and corporations for in-house business uses. Please read the [http://www.ks.uiuc.edu/Research/namd/license.html license] for additional information about NAMD. |
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= Usage = |
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== Loading the module == |
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You can load the default version of NAMD with the following command: |
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<pre> |
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$ module load chem/namd |
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</pre> |
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The module will try to load all modules (i.e., compiler, MPI, MKL) it needs to function. If loading the module fails, check if you have already loaded one of those modules, but not in the version required by NAMD. |
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If you wish to load another (older) version of NAMD, you can do so using |
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<pre> |
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$ module load chem/namd/<version> |
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</pre> |
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with <version> specifying the desired version. |
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Please cite NAMD in your publications according to the [http://www.ks.uiuc.edu/Research/namd/papers.html references]. |
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== Program Binaries == |
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The binary ''namd2'' is main program of the NAMD package. |
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<pre> |
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Usage: namd2 [+options] [config file] |
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Example: namd2 +isomalloc_sync run.namd |
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</pre> |
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For information about how to construct input files, please see the [http://www.ks.uiuc.edu/Research/namd/2.14/ug/ documentation]. |
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charmrun flipbinpdb flipdcd psfgen sortreplicas |
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=== GPU Acceleration === |
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Currently not available. |
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== Hints for using NAMD == |
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=== Parallel Execution === |
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It is usually more efficient to run several smaller jobs with reasonable speedup side by side. Check for a reasonable speedup by increasing the number of workers from 1, 2, 4, n cores. Do not forget to adjust the memory specification when changing the number of workers |
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=== Memory Management === |
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It requires some experience to choose the perfect memory value. Monitoring a job interactively may help to estimate the memory consumption. Requesting 1GB more than the required amount is typically sufficient. |
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=== Runtime Specification === |
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The wall-time limit is independent of the number of parallel workers. Selecting the best value requires some experience. In general, jobs with shorter wall times get higher priorities. It could help to run the job interactively for a small period of time to monitor its convergence. Furthermore, it may be advantageous to extrapolate the run time by looking at smaller test jobs. |
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= Examples = |
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As with all processes that require more than a few minutes to run, non-trivial compute jobs must be submitted to the cluster queuing system. |
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Example scripts are available in the directory <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$NAMD_EXA_DIR</span>: |
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<pre> |
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$ module show chem/namd # show environment variables, which will be available after 'module load' |
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$ module load chem/namd # load module |
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$ ls $NAMD_EXA_DIR # show content of directory $NAMD_EXA_DIR |
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$ cat $NAMD_EXA_DIR/README # show examples README |
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</pre> |
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Run a first simple example job: |
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<pre> |
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$ module load chem/namd # load module |
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$ WORKSPACE=`ws_allocate namd 3` # allocate workspace |
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$ cd $WORKSPACE # change to workspace |
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$ cp -a $NAMD_HOME/bwhpc-examples . # copy example files to workspace |
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$ cd bwhpc-examples/apoa1 # change to test directory |
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$ sbatch bwhpc_namd_apoa1.sh # submit job |
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$ squeue # obtain JOBID |
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$ scontrol show job <JOBID> # check state of job |
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$ ls # when job finishes the results will be visible in this directory |
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</pre> |
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= Useful links = |
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* [http://www.ks.uiuc.edu/Research/namd/2.14/ug/ Documentation (english)] |
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* [http://www.ks.uiuc.edu/Research/namd/mailing_list/ Maling list (english)] |
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* [https://en.wikipedia.org/wiki/NAMD Wikipedia article (english)] |
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* [https://de.wikipedia.org/wiki/NAMD Wikipedia article (german)] |
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---- |
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[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]] |
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Latest revision as of 16:35, 5 November 2021
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