BPTI

The simulation should be run from the directory bpti. This is standard example form NAMD User's guide. The Configuration file is given below.

#NAMD configuration file for BPTI
# molecular system
structure   bpti.psf
coordinates  bpti.pdb
# force field
paratypecharmm on
parameters par_all22_prot.inp
exclude scaled1-4
1-4scaling 1.0
# approximations
switching on
switchdist 8
cutoff 12
pairlistdist 13.5
margin 0
stepspercycle 20
#integrator
timestep 1.0
#output
outputenergies 10
outputtiming 100
binaryoutput no
outputname bptiout
dcdfreq 1000
#protocol
temperature 0
reassignFreq 1000
reassignTemp 25
reassignIncr 25
reassignHold 300
#script
minimize 1000
run 20000

To run this simulation issue the command

mpirun -np 16 /usr/local/namd/namd2mpi bpti.namd > bpti.log

We examine in the Bpti protein in this simulation. The system is initially at 0 K, which is then "heated" to 300 K in steps of 25 K every 1ps. The system is first minimized and then heating is performed. The simulation results can be viewed using mdanaly, a very simple shell script, for analysing Namdlog files.

./mdanaly bpti.log -np

Other analysis can be performed using the dcd trajectory file.Load the dcd trajectory file after loading the psf file to vmd.We can calculate the RMSD of protein trajectory. We use the script(rmsdnew.tcl) for the purpose.Issue the the command

 source rmsdnew.tcl

in the Extensions $>$ tkcon.The rmsd values are written to file rmsd.dat .