Scripts

A few scripts were needed to analyze the trajectory file .dcd from namd. We'll list here what we made and how they can be use.

RMSD along time

We used the RMSD to visualize if our simulation is reaching an equilibrium. It also helps a lot to see if the parameters are correctly set.

• Basically, this script will calculate the RMSD at each frame. The ouptut is residue number and the sum of its RMSD at each specified frame.
• You have to provide a list or residue id in the $sel_resid. There is no check for duplicated id, choose carefully your selection ;). (The .dcd and .pdb must be loaded before)
• The RMSD will calculate the RMSD for each non-hydrogen atom of the residue at each step and sum all these results. That's why the process is really heavy: #Residues * #AtomsPerResidue * #Frames * #CostOfRMSD

In the TkCon window type:

source residue_rmsd_v2.tcl

set sel_resid [[atomselect top "protein and alpha"] get resid] //select each residue composing the protein only once (only one CA...)

Remark: we updated the script residue_rmsd.tcl that was originaly available from namd website to be able to specify on which frames the rsmd has to be computed. Please have a look on this wiki for a more up-to-date version of the file... Command is:

rmsd_residue_over_time top $sel resid FIRST_FRAME LAST_FRAME