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VMD/NAMD System Preparation Tutorial

The necessary VMD files will be downloadable here.

Download the most recent version of the script called makefiles.tcl (check the date to confirm it’s the latest version). You will also need the .rtf and .str files in your working directory.

Required Files in Your Working Directory

Make sure the following files are in the same folder (your working directory):

  • makefiles.tcl (download from Drive)
  • Your .rtf file
  • Your .str file
  • Your .pdb file
  • Your .psf file

Editing the Script

Open makefiles.tcl in a text editor (e.g., VS Code).

Use the makegrid file is used to build a peptide grid in VMD using our L and D peptide systems.

  1. speciesL

  2. Type: String

  3. What it is: The name of your L-peptide structure (e.g., Lkyfil).

  4. speciesD

  5. Type: String

  6. What it is: The name of your D-peptide structure (e.g., Dkyfil).

  7. outputname

  8. Type: String

  9. What it is: The base name for the final output files (e.g., ion1to1kyfil).

  10. ratioL

  11. Type: Fraction

  12. What it is: The fraction of the total peptide count that will be L-peptides (e.g., 32/64 for 1:1).

  13. ratioD

  14. Type: Fraction

  15. What it is: The fraction of D-peptides (e.g., 32/64 for 1:1).

  16. totalpep

  17. Type: Integer

  18. What it is: The total number of peptides in your simulation (e.g., 64).

  19. gridX

  20. Type: Integer

  21. What it is: Number of peptides along the x-axis in the 3D grid.

  22. gridY

  23. Type: Integer

  24. What it is: Number of peptides along the y-axis.

  25. gridZ

  26. Type: Integer

  27. What it is: Number of peptides along the z-axis.

  28. Tip: gridX * gridY * gridZ should equal totalpep.

  29. unit_buffer

    • Type: Float (in Å)
    • What it is: The spacing between peptides in the grid.
    • Recommended: 32 Å depending on molarity.

  30. solvatePad

    • Type: Float (in Å)
    • What it is: The padding around the entire peptide box during solvation.
    • Recommended default: 5 Å.

If something does not work, use Ctrl + F and search for the variables above and hard code it into the script (not sure why some grids fail and others work).

Running the Script in VMD

  1. Open VMD

  2. Navigate to the Tk Console: Extensions > Tk Console

  3. Use the following commands to move into your working directory:

cd "folder_name"

Helpful navigation tips:

  • cd ../ — move back one folder level

  • pwd — print your current working directory

  • Load the script:

source makefiles.tcl
  1. Run the script:
makegrid LnewIons Lkyfil Lkyfil 64/64 0/64 64 4 4 4 32 5

Script may take a while as it loads the peptides. If it seems to fail, restart VMD and reload the script after hard coding values.

What This Script Does

This script will generate several intermediate .pdb and .psf files. The final outputs you care about are:

  • ionized.pdb
  • ionized.psf

Rename them to keep track of your peptide system. A good naming convention is:

ion<ratio><peptidename>.pdb

For example: ion1to1kyfil.pdb → Ionized file of KYFIL peptides with a 1:1 ratio of L and D stereochemistry.

Additional Output

You will also see a text file:

listofLD$molname.txt

This file contains:

  • Center of mass
  • Water sphere radius
  • Cell basis vectors
  • Center of the system
  • List of peptide names in the order they were created

This is important parameters that you need to copy and paste into the namd parameter files.

The necessary NAMD files will be downloadable here.

Required NAMD Files in Your Working Directory

Make sure the following files are in the same folder (your working directory):

  • Your .namd file
  • Your .prm file
  • Your .str file
  • Your .pdb file
  • Your .psf file

Editing .namd File

Find these variables and change it to your specific files.

structure          ionized.psf
coordinates        ionized.pdb

...

outputName         OutputName ;

...

# Periodic Boundary conditions, BE SURE TO CHANGE THIS FOR EACH PDB WILL BE DIFFERENT EVERY TIME YOU MAKE A NEW SYSTEM
cellBasisVector1 128.29100036621094 0 0
cellBasisVector2 0 128.47200202941895 0
cellBasisVector3 0 0 128.02500247955322
cellOrigin 47.1793327331543 48.19822311401367 48.779972076416016

...

run                 12500000    ;# 50 ns total trajectory therefore 2E+8 fs, but with 2 fs per step, 2E+8/2 = 50000000/2    steps

Editing .slurm File

Then submit this SLURM job script to run the full simulation:

#!/bin/bash
#SBATCH --nodes=7
#SBATCH --ntasks-per-node=36
#SBATCH --mail-user=zqp6mj@virginia.edu
#SBATCH --mail-type=END,FAIL,TIME_LIMIT
#SBATCH --time=1-00:00:00
#SBATCH --partition=parallel
#SBATCH -A  [ALLOCATIONS]
#SBATCH -o [OUTFILENAMEOFNAMDFILE].out

module load goolf namd
mpiexec namd2 [NAMEOFNAMDFILE].namd