<version_string> may deviate between the clusters. If you are missing a particular version, please inform us.
Both, VMD and NAMD, come with a license, which prohibits us to just install. We, therefore, need individual users to print and sign the linked licenses (VMD license and NAMD license) on that paper. Subsequently, send it via internal mail (“Hauspost”) to “ZDV HPC group”. We will then set the permissions accordingly.
When doing so, please include:
We generally do not provide support in using a particular software with all its flags (or in the case of a GUI, all its clicks). In this particular case we refer to the VMD tutorial.
That being written, we are aware that starting the VMD-GUI can be tricky and the relevant information hard to find.
Here, we give some brief snippets, covering the essentials:
$ module load vis/VMD # this will load the most current version, which is installed $ export VMDNOMPI=1
salloc. Here is a little more information on interactive jobs. With respect to the number of cpus: Not everything in VMD is parallelized. If you want to start an VMD-MPI job, you better write a VMD script and start VMD like a conventional MPI-application.
$ salloc -A <your_account> -p short -c <number_of_cpus> -t <sufficient_time> <snipping wainting for the session> $ srun vmd <arguments>
exitto relinquish the allocation.
Molecular Dynamics (MD) simulations can be tricky to be set up correctly. It is not unusual to make mistakes, which may consume lots of CPU time. The purpose of these snippets is not to teach running MD simulations in all detail, but to descript how to generate the most basic setup.
The following section refers to the VMD tutorial section on generating a PSF file:
This will create the following files:
Of course, VMD offers many more options, most are more sophisticated than this description.
With a given configuration file, you can start NAMD like this:
#!/bin/bash #SBATCH -t <time> #SBATCH -p <partition> # e.g. nodeshort / parallel #SBATCH -A <account> #SBATCH -N <rather start with a low number to test> #SBATCH -n <N * cores / node> module purge module load chem/NAMD # the suffix 'namd_conf' is arbitrary srun namd2 <prefix>.namd_conf
The configuration file content depends on the simulation to be carried out, however, the
structure parameters could simply refer to the autogenerated
.psf files produced by VMD as described, respectively.