This directory contains six files:

1. mkpsf_bnm.tcl -- this is the VMD/psfgen script that creates the first vacuum psf/pdb pair.
2. my_bnm_vac.namd -- this is a NAMD configuration file used to relax the "guessed" coordinates resulting from step 1.
3. my_bnm_solv.tcl -- this is a VMD script that uses solvate and autoionize to generate a neutralized, solvated MD system using the coordinates from step 2 as input.
4. my_bnm_solv_stageN.namd -- this is a NAMD configuration file template for a set of MD stages that equilibrates the solvated system. Since the system is rather small, the barostat shrinks the volume is such a way that the patch grid is invalidated early on.
5. V.gp -- gnuplot script for plotting volume vs timestep during to solvated MD
6. do_test.sh -- this BASH script does everything

Make sure PSFGEN_BASEDIR resolves to the root directory of your local copy of this repository (mine is ${HOME}/research/psfgen). It is also assumed below that CHARMRUN resolves to your local charmrun executable and NAMD2 resolves to your local namd2 executable. For me, these are ${HOME}/namd/NAMD_2.12_Source/Linux-x86_64-g++/charmrun and ${HOME}/namd/NAMD_2.12_Source/Linux-x86_64-g++/namd2.

1. Execute do_test.sh a clean directory

$ mkdir bnm
$ cd bnm
$ $PSFGEN_BASEDIR/bnm/do_test.sh

The resulting files sol-stage2.coor, sol-stage2.vel, and sol-stage2.xsc are the coordinates, velocities, and extended-system files of after the final equilibration stage. The final coordinates of just the BNM-III-170 molecule are stored in my_bnm_x.pdb.

This uses the file bnm.str in $PSFGEN_BASEDIR/charmm, which was generated using the CGenFF server from a PDB of the residue 5VG from 5f4p.pdb. bnm.str only has IC's for placing hydrogen atoms; you can't use it to grow a whole BNM molecule if any heavy atoms are missing.

2018, Cameron F Abrams