VMD+NAMD

Licensing Issues #

We have setup and compiled VMD and NAMD for you – and we will continue to do so for new versions upon request. You will find the installed modules as

vis/VMD/<version_string>
chem/NAMD/<version_string>

Here, the <version_string> may deviate between the clusters. If you are missing a particular version, please inform us.

Using VMD #

That being said, we are aware that starting the VMD-GUI can be tricky and the relevant information hard to find.

Starting the graphical user interface (GUI) #

Here, we give some brief snippets, covering the essentials:

• First, you need to load the module and instruct VMD to start in its graphical, non-MPI mode:

module load vis/VMD # this will load the most current version, which is installed
export VMDNOMPI=1

• Next, start an interactive session, e.g. with salloc. Here is a little more information on interactive jobs (broken link). 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 (broken link).

salloc -A <your_account> -p smp -c <number_of_cpus> -t <sufficient_time>
  <snipping waiting for the session>
srun vmd <arguments>

• When ending the session, do not forget to type exit to relinquish the allocation.

Setting up a simulation file for NAMD #

Generating .psf files #

A .psf (protein structure file) is needed to feed NAMD. Beginners frequently have troubles generating one.

The following section refers to the VMD tutorial section on generating a PSF file:

1. load a new molecule
2. run the autopsf utility (Extensions -> Modeling -> Automatic PSF Builder)

This will create the following files: <molecule_prefix>_autopsf_formatted.pdb, molecule_prefix>_autopsf.log, <molecule_prefix>_autopsf.pdb, <molecule_prefix>_autopsf.psf.

Of course, VMD offers many more options, most are more sophisticated than this description.

Periodic boundaries: Estimating Unit Cell Size #

To run a simulation with periodic boundaries, we assume that you have loaded the desired .pdb file into VMD and set to calculate the unit cell:

Within VMDs Tk Console¹ you can run:

set everyone [atomselect top all]
measure minmax $everyone

This will yield two vectors, e.g.: {-38.473999 -24.975999 -35.2630} {36.910999 29.686 35.957}. To obtain the values for the initial(!) cellBasisVector-entries you need to add together the absolute values, e.g. abs(-38.473999) + 36.910999 = 75.384998. Subsequently set the cellBasisVector-entries to sensible (slightly rounded) values, such that the result vector of your addition becomes the diagonal:

cellBasisVector1     75.385 0.0 0.0
cellBasisVector2     0.0 54.662 0.0
cellBasisVector3     0.0 0.0 71.22
cellOrigin           0.0 0.0 0.0

Finally, turn on PME-settings and set the box size, such that the initial conformation will surely fit, e.g.:

PME                  on
PMEGridSizeX         80
PMEGridSizeY         60
PMEGridSizeZ         75

Using NAMD #

With a given configuration file, you can start NAMD like this:

#!/bin/bash

#SBATCH -t <time>
#SBATCH -p <partition> # e.g. 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 coordinates and structure parameters could simply refer to the auto-generated .pdf and .psf files produced by VMD as described, respectively.

CHARMM force fields #

The NAMD tutorial indicates this download site for CHARMM force fields and topology files (We indicate this as searching can be tedious.)

When using these force field files, be sure not to forget to amend the force field type to the configuration file, e.g.:

parameters           <path to desired prm>.prm
paraTypeCharmm       on

Footnotes #