NAMD

class NAMD

This interface currently works as both an MD driver and an MM energy evaluator for MD simulations with the NAMD molecular dynamics simulation package (version 2.14 or later)

As a MM interface, the options described in MM interfaces are available, as well as the NAMD specific options outlined below.

A NAMD Theory object can be specified as follows:

my_namd = NAMD(frag=...,
               par=...,
               pdb=...,
               psf=...,
              )

which would then be called as theory=namd and driver='namd' in a subsequent MD task:

md = MD(theory=namd,
        freq_dcd=...,
        freq_chk=...,
        driver='namd',
        minimise=...,
        nsteps=...,
        nsnapshots=...,
        timestep=...,
        temperature=...,
        boundary=...,
       )

md.run(dryrun=False)

Note

The NAMD interface is not currently compatible with other tasks such as SP() or Opt(). This support will be added in a future release of ChemShell.

General options

binary: (default: True) NAMD outputs in binary format

coor: (default: '_namd.coor') Filename of binary coordinates a restarted job runs from

input: (default: '_namd.inp') Input script’s filename

margin: (default: 4.72432 Bohr) This parameters affects only the performance. Defaulted to 0.0 in NAMD, see: NAMD Manual

output: (default: '_namd.out') Output filename

par

(default: '') Forcefield parameters filename(s). Allowed types of value are:

A Python str of a single filename
A Python list of multiple filenames. They will be concatenated by ChemShell to generate a single file

pdb: (default: '') PDB filename for input structure

prefix: (default: '_namd') Prefix for the .coor (coordinates) and .vel (velocity) filenames

prefix_restart: (default: '_namd') Prefix for files (.coor, .vel, and .xsc) from which a job is to restart

psf: (default: '') Name of PSF file to use. This does not need to be specified if the NAMD.psfgen() method has been run beforehand

psfgen_options: (default: {}) Keyword option(s) for the PSFGEN interface (see NAMD.psfgen() below). The PSFGEN keywords must be given as str, for example, psfgen_options={'residue_aliases':{'CMO':'CO'},'topologies':['camphor.rtf']}

vel: (default: '_namd.vel') Filename of the velocity file

xsc: (default: '_namd.xsc') Filename of the extended system configuration (XSC)

xst: (default: '_namd.xst') Filename of the extended system trajectory (XST)

Forcefield options

cutoff: (default: 22.6767 Bohr) Cutoff distance for electrostatic and van der Waals interactions. Default equals to 12.0 Å.

exclude: Choose a type to be excluded from non-bonded interactions. Accpeted values are: 'none', '1-2', '1-3', '1-4', or 'scaled1-4'

ff_dir: (default: '') Directory containing topology and parameter files. If left blank it will be chosen to be the built-in library of ChemShell’s default forcefield CHARMM.

freq_nonbonded: (default: 1) Frequency to evaluate non-bonded interactions

freq_full_elect: (default: 1) Frequence to evaluate electrostatic interactions

merge_cross: (default: True) Merge the crossterm (or CMAP) contribution into the dihedral energy

pairlist_dist: (default: 26.4562 Bohr) Distance criterion to generate pairs of atoms with electrostatic and van der Waals interactions. Default equals to 14.0 Å.

scaling14: (default: 1.0) Scaling factor for 1-4 interactions

switching: (default: True) Apply smoothing functions to the electrostatic and van der Waals interactions

switch_dist: (default: 18.8973 Bohr) Distance to start applying the smooothing functions. Default equals to 10.0 Å.

MD options

nsteps_per_cycle: (default: 1) Number of timesteps between cycles of atom reassignments

seed: (default: 12345) Seed number for the random number generator if temperature or langevin is selected

Constrains

constraints: (default: '') Filename (in PDB format) of constraints definition

constraints_ref: (default: '') Filename (in PDB format) of a reference structure without constraints

fixed_atoms: (default: '') Filename (in PDB format) of a structure with fixed atoms (b-factors are 1.0)

fixed_atoms_forces: (default: True) Toggle computation of interactions between fixed atoms

Pressure control

constant_area: (default: False) Keep the ratio of the unit cell in the x-y plane constant while allowing fluctuations along all axes. See NAMD Manual

flexible_cell: (default: False) True allows the three orthogonal dimensions of the periodic cell to fluctuate independently. See NAMD Manual

group_pressure: (default: False) Calculate the pressure using hydrogen–group—based pseudo-molecular virial and kinetic energy. Only valied when the rigid bonds model (SHAKE) is used

Periodic boundary conditions

pme: (default: True) Toggles the particle mesh Ewald (PME) method

pme_grid_sizes: (default: [0,0,0]) Can be a list, tuple, or NumPy array of size 3. The values must be divisible by 2, 3, and 5 at the same time. If left undefined they will be determined by ChemShell.

wrap_all: (default: True) Output coordinates by wrapping all atoms within the periodic simulation box

wrap_water: (default: True) Output coordinates by wrapping water molecules within the periodic simulation box

PSFGEN options

The PSFGEN plugin is available with NAMD. To use it in ChemShell, run the member function of a created NAMD instance:

my_namd.psfgen(my_biofrag, ...)

NAMD.psfgen(bioFrag, allow_undefined=False, atom_aliases={}, dryrun=False, ff='charmm', ff_dir='', guess_coord=True, haem='', ignore_undefined=True, input='_psfgen.inp', merge_solvents=False, no_auto=[], output='_psfgen.out', output_pdb='', output_psf='', output_dir='_psfgen', override_standard=False, patch=True, patch_disulphides=True, patch_titratables=True, path='', residue_aliases={}, solvents=[], topologies=[], use_newer_version=True)

Parameters:

bioFrag (Fragment) – The biomolecular fragment (typically created from PDB/PQR/PSF)
allow_undefined (bool, optional) – Tolerate with undefined residues
atom_aliases (dict, optional) – Atom names to be aliased
dryrun (bool, optional) – To generate the input script only without really executing PSFGEN
ff (str, optional) – Forcefield scheme name (we currently only support CHARMM-type forcefield)
ff_dir (str, optional) – Path to forcefield data if the ChemShell built-in ones should be overridden
guess_coord (bool, optional) – Let PSFGEN guess positions of the missing atoms
haem (str, optional) – Residue name of the haem in case there is one and ChemShell cannot recognise it
input (str, optional) – Filename of the PSFGEN input script
merge_solvents (bool, optional) – Merge solvents to a single segment (Use with caution because it may cause the resIDs to exceed the 9999 limit!)
no_auto (list, optional) – Name(s) of segments for which automatic angles/dihedrals assignment should not apply. They are solvents by default (no_auto=[])
output (str, optional) – Name of the PSFGEN output file
output_pdb (str, optional) – Name of the resulting PDB file. It is _TITLE_psfgen.pdb by default where TITLE is bioFrag’s title string
output_psf (str, optional) – Name of the resulting PSF file. It is _TITLE_psfgen.psf by default where TITLE is bioFrag’s title string
output_dir (str, optional) – The subdirectory where the PSFGEN output files are generated
override_standard (bool, optional) – Data from ChemShell’s built-in library will override the standard forcefield data (currently CHARMM-type only) if override_standard=True
patch (bool, optional) – Patch residues
patch_disulphides (bool, optional) – Patch the disulphide bonds
patch_titratables (bool, optional) – Patch the titratable amino acids
patch – Apply residue patches via PSFGEN
path (str, optional) – Path to the PSFGEN executable if the current ChemShell installation does not have NAMD
solvent (list, optional) – Extra name(s) of solvent segments in addition to the ChemShell-recognisable names (currently water only such as ‘CW’, ‘SOLA’, ‘SOLB’,…)
topologies (str or list, optional) – Extra topology file(s) (.rtf)
use_newer_version (bool, optional) – Use the one of the newer version if multiple topologies (.rtf) files containing definitions of same residues are chosen. For example, ChemShell may suggest top_all22_prot.rtf and top_all36_prot.rtf at the same time, but the latter will be used if use_newer_version=True