HPC:NAMD
From HPC wiki
NAMD
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
NAMD module usage
To check available versions of NAMD, run the "module avail" command:
[asrini@node155 ~]$ module avail --------------------------------------------------------------------------------- /usr/share/Modules/modulefiles ---------------------------------------------------------------------------------- AllPaths-LG-v49967 bzip2/1.0.6 gcc/8.3.1 NAMD-2.9-Linux-x86_64-multicore R/3.1.1 samtools-1.1 autoconf/2.69 CASAVA/v1.8.2 gsl-2.1 ngsutils-0.5.7 R/3.1.2 scons/2.3.1 automake/1.15 cellranger/5.0.1 hdf5/1.8.21 null R/3.2.1 SOAPdenovo2-r240 bamtools/2.3.0 circos/0.67-5 homer-v4.6 pandoc/2.0.6 R/3.2.2 STAR/2.3.0e bcftools/1.11 cmake/3.21.1 htslib/1.11 pandoc/2.3 R/3.3.0 STAR/2.4.1d bcl2fastq2/v2.15.0.4 cufflinks-2.2.0 java/openjdk-1.6.0 parallel/20201122 R/3.3.1 STAR/2.5.2a bcl2fastq2/v2.16.0.10 cufflinks-2.2.1 java/openjdk-1.7.0 pcre-8.38 R/3.4.2 STAR/2.7.1a bcl2fastq2/v2.17.1.14 curl-7.49.0 java/openjdk-1.8.0 perl5lib R/3.4.3 texinfo/6.0 bcl2fastq2/v2.19.0.316 dot julia/1.0.5 picard/1.96 R/3.5.1 texlive-20170214 bcl2fastq2/v2.20.0.422 EMBOSS-6.6.0 julia/1.4.2 picard-tools-1.141 R/3.6.3 Trimmomatic-0.32 bcl-convert/3.8.2 eQtlBma-1.2.2 ld-library-path pkg-config-path R/4.0.2 trinity-r20140717 blat-v35 eQtlBma-1.3.1 libtool/2.4.6 plink-1.90b3b rclone/1.47.0 use.own boost/1.55.0 FastQC-0.11.2 local_coreutils-8.24 python/2.7.9 RUM/2.0.5_06 wget/1.20.3 boost/1.57.0 fastx_toolkit-0.0.14 manpath python/3.6.3 sailfish/0.6.3 WiggleTools/1.0 bowtie2/2.1.0 gcc/5.3.1 module-git python/3.9.1 samtools/1.11 zlib/1.2.8 bowtie2/2.3.4.1 gcc/6.3.1 module-info qiime/1.8.0 samtools-0.1.18 bwa-0.7.10 gcc/7.3.1 modules QTLtools/1.3.1-11 samtools-0.1.19 ---------------------------------------------------------------------------------------- /etc/modulefiles ----------------------------------------------------------------------------------------- mpi/mpich-3.0-x86_64 mpi/mpich-3.2-x86_64 mpi/mpich-x86_64
To load/use one of the available NAMD modules run the "module load" command (click "expand" to see basic module usage):
[asrini@node155 ~]$ module load NAMD-2.9-Linux-x86_64-multicore [asrini@node155 ~]$ which namd2 /opt/software/NAMD/NAMD_2.9_Linux-x86_64-multicore/namd2
