NAMD performance graphs

Graphs of NAMD performance. The explicit-solvent system has: 47,481 atoms, PME electrostatics, and a 4 fs timestep. These simulations were performed on a 12-core workstation with Xeon E5-2680 CPUs and three GeForce GTX 960 graphics cards. Simulations were performed with NAMD 2.12 (pre-compiled Linux-x86_64-multicore-CUDA or Linux-x86_64-multicore builds) unless otherwise noted.


Complete set of files for calculating Ramachandran free-energy landscape of alanine dipeptide on graphene.

Ready-to-run NAMD configuration file: PhiPsi/namd/abf_graph_alad_36m.0.namd
Download files:

Complete set of files for calculating free-energy of adsorption of m-cresol to hydroxylated graphene.

Ready-to-run NAMD configuration file: GraphOhOh/namd/abfFreeTop_3_15_ohoh_bPh.0.namd
Download files:

DiffusionFusion: a program for calculating position-dependent diffusivity from molecular dynamics trajectories

This code, which works for both conventional and fractional-order Smoluchowski models is available on our GitHub page.
The approach is described in DOI: 10.1038/srep35913 and 10.1021/ct300867e

Using Martini polarizable water with NAMD

PSF File: cg_polar_water.psf
PDB File: cg_polar_water.pdb
CHARMM-style parameter file: martini_pol_water.par
Example NAMD config file: namd_waterP1.namd
Script for building the PSF and PDB above: makeMartiniPolarWater.tcl

Necessary NAMD modifications:

Change the following line in Molecule.C

} else if (atoms[atom_number-1].mass <=3.5) {
} else if (atoms[atom_number-1].mass <=3.5 || strcmp(atom_type,"D")==0 ) {

Comment out this splitPatch line SimParameters.C

else if (!strcasecmp(s, "1-2"))
    exclude = ONETWO;
    //splitPatch = SPLIT_PATCH_POSITION;

Comment out this line in SimParameters.C:

//NAMD_die("Do not use Particle Mesh Ewald with Martini.  Set: PME off");