Scripts

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

Extract data from namd log file

Some informations about the simulation are stored in the log file. A script is really useful to extract them before plotting. We updated the file available on namd website. Here is our version of namdstats.tcl. Please rename to namdstats.tcl after download.

Here are the steps to use this script:

source namdstats.tcl

data_time DATA_NAME LOG_FILE

It will extract data from LOG_FILE, creating a DATA_NAME.dat in the working directory (type pwd to see where you are) containing values and time informations.

Available DATA_NAME are: BOND, ANGLE, DIHED, IMPRP, ELECT, VDW, BOUNDARY, MISC, KINETIC, TOTAL, TEMP, TOTAL2, TOTAL3, TEMPAVG, PRESSURE, GPRESSURE, VOLUME, PRESSAVG, GPRESSAVG.

So, to extract pressure from our first simulation, the command is:

data_time PRESSURE namd_log

Sum of RMSD for each residue

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