Trajectory Analysis: traj.inp

Parameters to charmm:

parameters	options	default
pdbfile=	root of pdbfile name also segid of protein	none, die
toppar=	path to topology and parameter files	$toppar
crystal=	true, false	false
shape=	cubic, octahedral	cubic
begin=	number	1
end=	number	10
current=	number	@begin
status=	start, restart	start
water=	true, false	false
task=	format, unformat,unmerge, stripwat, atomrms, timerms, p2	none, die

Required files and directories:

@toppar/top_all22_prot.inp
@toppar/par_all22_prot.inp
@pdbfile.psf
@pdbfile_dimens.stream
cubic.xtl or rhomba.xtl
merged crd files of the form @pdbfile_e1-8.crd

TASKS

Strip Water from trajectory
RMSD (atomic fluctuations)
RMSD time series of average RMSD for whole protein
P2 correlation .
Order parameters .
Energy, Temperature, Density time series

Strip Water

% cd crd
% ln -s ../1fsc_dimens.stream ../1fsc.psf .
% setenv toppar ".."
% charmm pdbfile=1fsc begin=1 end=8 task=stripwat \
 < ../traj.inp > stripwat.out

gives output files:

stripwat.out charmm output
1fsc_e1-8_nowat.crd trajectory with no water
1fsc_nowat.pdb pdb file with no water
1fsc_nowat.psf psf file with no water
1fsc_nowat.crd pdb file with no water

RMSD: average rmsd of each atom position vs average structure

% cd crd
% ln -s ../1fsc_dimens.stream ../1fsc.psf .
% setenv toppar ".."
% charmm pdbfile=1fsc begin=1 end=8 task=atomrms \
 water=true < ../traj.inp > atomrmsd.out

gives output files:

atomrmsd.out charmm output
1fsc_e1-8.rms rms file suitable for plotting
1fsc_e1-8.avgdmb average coord in "dumb" format
1fsc_e1-8.avgcrd average coordinates in charmm coord format

We can plot the rmsd with xmgr an make the following plot (saved xmgrace file)

% xmgrace 1fsc_e1-8_nowat.rms

From this figure it is clear that the water is very mobil and not really worth examining with respect to rmsd motion. We use the water=false argument in the charmm command line for the traj.inp script or leave it out since it is default:

% charmm pdbfile=1fsc begin=1 end=8 task=atomrms \
 < ../traj.inp > atomrmsd_nowat.out

gives output files:

atomrmsd_nowat.out charmm output
1fsc_e1-8_nowat.rms rms file suitable for plotting
1fsc_e1-8_nowat.avgdmb average coord in "dumb" format
1fsc_e1-8_nowat.avgcrd average coordinates in charmm coord format
```
% xmgrace 1fsc_e1-8_nowat.rms
```