% cd crd% ln -s ../1fsc_dimens.stream ../1fsc.psf .
% setenv toppar ".."
% charmm pdbfile=1fsc begin=1 end=8 task=timerms \
< ../traj.inp > atomrmsd.out
gives output files:1fsc_e1-8_nowat.trms
- 1fsc_e1-8_nowat.trms.out charmm output
- 1fsc_e1-8_nowat.trms_dumb rms file dumb format
- 1fsc_e1-8_nowat.trms_card rms file card format
- 1fsc_e1-8_nowat.trms rms file suitable for plotting
We can plot the rmsd with xmgr an make the following
plot (saved xmgrace file)
% xmgrace 1fsc_e1-8_nowat.trms
From this plot it is apparent that the structure has most likely stabilized after around 500 ps.