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This section details the steps required to run MD using NAMD-Lite with the MIST library.

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Running NAMD-Lite with MIST

There is extensive help on using NAMD-Lite on the NAMD website, however, this provides a quick start for using NAMD-Lite with the MIST plugin. It is not intended to replace a good working knowledge of NAMD-Lite and its uses.

Supported functionality

Not all of the functionality available to NAMD-Lite users, even more so with NAMD, is available when using the MIST library. We recommend using NAMD-Lite/NAMD without MIST when you need particular functionality and switching to your designed integrator using MIST for production runs. The main restrictions are:

  • Thermostats: thermostats (tcoupl) are currently not supported.
  • Constraints: constraints (SETTLE) are currently not supported.

Using mdsim

The mdsim program, see the mdx documentation page (mdx is the old name for the NAMD-Lite distribution) for an overview, performs an MD simulation using a subset of what is available to NAMD It reads in simulation parameters from a *.config file.

For this example we shall be looking at the adp example in the repository:

We need to get some files (do this outside the MIST root):

mkdir adp
cd adp
wget https://bitbucket.org/extasy-project/mist/raw/master/examples/namd-lite/adp/adp.config
wget https://bitbucket.org/extasy-project/mist/raw/master/examples/namd-lite/adp/adp.params
wget https://bitbucket.org/extasy-project/mist/raw/master/examples/namd-lite/adp/adp.psf
wget https://bitbucket.org/extasy-project/mist/raw/master/examples/namd-lite/adp/adp.pdb

For the MIST-extended version it is necessary to add the parameter mist, and either if it is to be used (on) or not (off), to the configuration file. Add the following line anywhere to the adp.config file:

# integrator params          
 mist on

You will also have to add a mist.params file. The basic file should contain:

# Select which integration algorithm to use                                               
integrator verlet

# Parameters for the integrator                                                           
# none
where verlet is replaced by your choice of integrator. A list of the available integrators and parameters required for any integrators is discussed in the next section.

The next step is to run your MD job, using the MIST library and the correct configuration file: 

/path/to/namd-lite/install/mdsim myconfig.config

You should see output like:

# deven started successfully
# attempting to read parameter file as X-Plor format
# attempting to read parameter file as CHARMM format
# force field parameters file "./adp.params"
# PSF file "./adp.psf"
# successfully combined force field parameters with topology
# system has:        22 atoms
#                    21 bonds
#                    36 angles
#                    41 dihedrals
#                     4 impropers
#                     0 explicit nonbonded exclusions
# PDB coordinates file "./adp.pdb"
#STEP: 63 degrees of freedom
# grid cells:  1 (nonperiodic) by 1 (nonperiodic) by 1 (nonperiodic)
# overall density is 22 atoms per grid cell
#STEP: Running velocity-Verlet for 10 steps...
# step       energy         temp           ke           pe         bond
     0    11.106269   327.128857    20.477127    -9.370858     3.374783
     1    11.171478   308.058010    19.283358    -8.111880     4.357899
     2    11.320627   258.426597    16.176605    -4.855977     6.273552
     3    11.406834   211.436801    13.235207    -1.828374     7.362260
     4    11.361021   187.103537    11.712030    -0.351009     6.861832
     5    11.270724   177.010321    11.080229     0.190495     5.857831
     6    11.270453   162.839982    10.193216     1.077237     5.936446
     7    11.371656   145.022839     9.077925     2.293731     7.215299
     8    11.444270   145.068298     9.080770     2.363500     8.162533
     9    11.378642   177.741090    11.125973     0.252669     7.476510
    10    11.227537   227.758660    14.256899    -3.029362     5.731906
# deven stopped successfully
# total wall-clock time: 0.028755 seconds
#
# Success!
#
which gives you a basic overview on how to set NAMD-Lite to work with MIST.

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