Using NAMD with Alces Flight Compute¶
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems . The following page details how to install the NAMD application to your Alces Flight Compute environment, as well as how to get started using the NAMD application.
From your Alces Flight Compute environment, you can begin by installing the NAMD Gridware package. Use the command below to install NAMD:
alces gridware install apps/namd --variant all --yes
Download and unpack the following tutorial files to your home directory:
The tutorial files contain the appropriate files to get started with NAMD - examining the minimisation and equilibration of ubiquitin protein in a water sphere placed in vacuum.
The tutorial files can be downloaded and unpacked to your cluster using the following commands from the login node:
wget https://s3-eu-west-1.amazonaws.com/alces-public/namd-tutorial-files.tgz tar -zxvf namd-tutorial-files.tgz cd namd-tutorial-files/1-2-sphere
Next, start a GNOME desktop session and connect to it to begin using NAMD/VMD . This can be done from the login node with the following command:
alces session start gnome
Once you are connected to your graphical desktp session, open the Terminal application and load the following modules :
module load apps/namd_mpi
Next, navigate to the previously unpacked tutorials directory then navigate to the
1-2-sphere directory. Open the
ubq_ws_eq.conf configuration file for editing in your favourite text editor, then check that the
coordinates paths are correct.
Next, run the simulation - this should take about 20 minutes to complete. You can either run this through an interactive scheduler session on a dedicated compute node or create a job script and run through the cluster scheduler.
To run the NAMD simulation in an interactive session using the SGE scheduler - run the following commands:
qrsh -pe smp-verbose 2 -l h_vmem=1G cd namd-tutorial-files/1-2-sphere module load apps/namd_mpi mpirun -np 2 namd2 ubq_ws_eq.conf > ubq_ws_eq.log &
Or to run through the job scheduler, you could use the following example job script for the SGE scheduler:
#!/bin/bash -l #$ -pe mpislots-verbose 4 #$ -l h_vmem=1G #$ -N NAMD -o $HOME/namd.$JOB_ID.out module load apps/namd_mpi cd $HOME/namd-tutorial-files/1-2-sphere mpirun namd2 ubq_ws_eq.conf
Once the task has finished, your output file will contain lots of output data. The end of your output file should contain the following if the job has successfully completed:
WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 2600 WRITING COORDINATES TO OUTPUT FILE AT STEP 2600 CLOSING COORDINATE DCD FILE The last position output (seq=-2) takes 0.046 seconds, 309.516 MB of memory in use WRITING VELOCITIES TO OUTPUT FILE AT STEP 2600 The last velocity output (seq=-2) takes 0.015 seconds, 309.516 MB of memory in use ==================================================== WallClock: 269.963684 CPUTime: 269.963684 Memory: 309.515625 MB End of program
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|||Starting desktop sessions|
|||Loading environment modules|