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
2. mini-2.config: fix water
3. mini-3.config: fix protein backbone (double check)

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 depend on [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