Tips

Installation

• Compile (Makefile)

Molecular dynamics

Coarse-grained MD

• Preparing an initial configuration (GenCGconf)
• Parameter and topology files
• How to treat the colloidal particles

All-atom MD

Free energy analysis during MD

• Calculating PMF using constraint MD
• Calculating PMF using steered MD

Analysis

• How to read trajectry files from NAMD (dcd) or GROMACS (xtc, trr).

Free energy analysis using "Energy Representation Method"

• Compile with

How to read trajectry files from NAMD (dcd) or GROMACS (xtc, trr).

You can read a variety types of trajectory files such as dcd (NAMD standard) and xtc, trr (GROMACS standard) and so on, using "molfile" library, which is the library used in "vmd". Thanks to the program written by Dr. Axel Kohlmeyer, we can use molfile libraries as a plugin from MPDyn. To use this, we have to remake a binary module, "MPDynS_MOLFILE", using Makefile.molfile.intel9 (this is basically written for intel compiler ver.9.1).

# make -f Makefile.molfile.intel9 clean
# make -f Makefile.molfile.intel9

Then, you will find "MPDynS_MOLFILE" in ../bin/.

To specify the type of the trajectory file you want to analyze, the keyword "DATA_FORM_TRJ" should be used in the jobscript file, "input.data".