How to run a regular NPT simulation

Preparation

Create pdb, psf, force-field and NAMD config files. The first two could be created by VMD, starting from downloading pdb file from pdb.org webpage. NAMD configuration files include energy minimization, heating, pre-equilibrium, constraints, and non-biased NPT files.

Minimization

1. mini-1.config: fix protein and/or membrane atoms (10000 CG steps)

   VMD selection text: protein

2. mini-2.config: fix water and backbone (100000 CG steps)
   • If still not stable after certain time especially jumping between two values [1], run 50000 more SD steps

   VMD selection text: water or backbone

3. mini-3.config: fix water only (100000 CG steps)
   • If still not stable after certain time, run 50000 more SD steps

   VMD selection text: water

4. mini-4.config: fix nothing (50000 CG steps)
   • If still not stable after certain time, run 50000 more SD steps

   fixedAtoms off

For instance, the spring constant is 5.0

Heating

Heat up the system from 0K to 310K

Pre-Equilibrium

NPT with constraints, for instant, the spring constant is 5

Constrains

Step-wisely release constraints from 5 to 0, and release the constrained atom range from all to backbone to CA atoms.

Regular NPT/NVT Simulations

Attach a configure file.

Good habits

• mkdir run
• cd run
• mkdir output
• Create your namd parameter file here
• Remember to specify output path to ./output/xxxx
• mkdir analysis
• mkdir analysis/result
• cd analysis
• Create your rmsd calculation script (usually tcl)
• Remember to specify output path to ./result/xxxx
• cd ..
• Create your job script here
• Remember to specify standard output to ./output/xxxx
• Remember to add execution of rmsd calculation
• qsub job.sh
• Your output and log file will show up in ./output
• After MD finishes, torque stdout will show up in the submitting directory
• RMSD will be calculated afterwards and result shows up in analysis/result

You should understand all these steps and add any desirable analysis that you want it to be automatic.

Common Errors or Frequent Questions

MD parameters that must be multiple of [steppercycle]

Be caution that nearly all output file writing must a multiple of [steppercycle] as most of the integrator does not integrate every step and they only have things to write at the step which calculation actually was performed: restartfreq
dcdfreq (of course also xstfreq veldcdfreq)
outputenergies (of course also outputpressure)
SMDoutputfreq