Hi,
If I am performing an MD Simulation in which the two groups/molecules are moving in a direction on applying a force on the system, how would I calculate the velocities/acceleration of the two?
How would one figure it out which one is moving faster except from visualizing?
Any small suggestion will be quite helpful.
Thanks
To expand a bit on Martin's suggestion, in VMD one can write scripts to do most anything. After reading in the trajectory file, you could
set mol1 [atomselect top "define your first molecule"]
set mol2 [atomselect top "define your second molecule"]
to define the molecules. Then, for each frame f in the trajectory that you want to
analyze (not necessarily each time step)
set x1($f) [measure center $mol1]
set x2($f) [measure center $mol2]
This will provide you with the center of mass of each molecule and will create two (three-dimensional) arrays. You can write them to a file and plot them or compute velocities and accelerations by differencing within VMD:
set dx1($f) [vecsub $x1($f) $x1($f-1)]
set v1mag($f) [expr [veclength $dx1($f)] / $deltat ]
etc., where deltat is the time step between frames.
Note that differencing will amplify noise, so you will need filtering of some form or another to make sense of the output. You may also want to consider just the component of velocity along the direction of your applied force. That would simplify some of the calculations.
Other analysis packages provide similar capabilities.
Knowing the distance traveled and the time elapsed means knowing the average velocity.
To expand a bit on Martin's suggestion, in VMD one can write scripts to do most anything. After reading in the trajectory file, you could
set mol1 [atomselect top "define your first molecule"]
set mol2 [atomselect top "define your second molecule"]
to define the molecules. Then, for each frame f in the trajectory that you want to
analyze (not necessarily each time step)
set x1($f) [measure center $mol1]
set x2($f) [measure center $mol2]
This will provide you with the center of mass of each molecule and will create two (three-dimensional) arrays. You can write them to a file and plot them or compute velocities and accelerations by differencing within VMD:
set dx1($f) [vecsub $x1($f) $x1($f-1)]
set v1mag($f) [expr [veclength $dx1($f)] / $deltat ]
etc., where deltat is the time step between frames.
Note that differencing will amplify noise, so you will need filtering of some form or another to make sense of the output. You may also want to consider just the component of velocity along the direction of your applied force. That would simplify some of the calculations.
Other analysis packages provide similar capabilities.
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