Difference between revisions of "How to run a regular NPT simulation"

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==Regular NPT/NVT Simulations==
 
==Regular NPT/NVT Simulations==
 
Attach a configure file.
 
Attach a configure file.
 +
 +
==Good habits==
 +
*<code>mkdir run</code>
 +
*<code>cd run</code>
 +
*<code>mkdir output</code>
 +
*Create your namd parameter file here
 +
*Remember to specify output path to ./output/xxxx
 +
*<code>mkdir analysis</code>
 +
*<code>mkdir analysis/result</code>
 +
*<code>cd analysis</code>
 +
*Create your rmsd calculation script (usually tcl)
 +
*Remember to specify output path to ./result/xxxx
 +
*<code>cd ..</code>
 +
*Create your job script here
 +
*Remember to specify standard output to ./output/xxxx
 +
*Remember to add execution of rmsd calculation
 +
*<code>qsub job.sh</code>
 +
*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.

Revision as of 00:04, 6 August 2014

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.

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