[gmx-users] Determining Force and torque of a group of atoms
akari karin
j.akarikarin at gmail.com
Wed Nov 5 16:08:09 CET 2014
Dear gromacs users,
I am trying to measure the torque acting on a group of atoms in my system.
I am trying to approach the problem is either of the two ways-
a)
1. Calculate the Force acted in each atoms in the group (F)
2. Calculate the position of the atoms in the group (r)
3. From the formula, Torque= r cross F, calculate the torque.
b)
1. Calculate the velocity of each atoms (v) .
2. Calculate the position of each atoms (r).
3. From the formula, angular velocity = v* r
4. Differentiate angular velocity and get the angular acceleration (alpha)
5. Calculate the Moment of inertia of the group (I)
6. Multiply the Moment of inertia and the angular acceleration (as Torque =
I*alpha)
Calculate the torque for each atom in either of the methods (a) or (b).
Total torque = sum of all the torques of the atoms in the group
Either way, I need at least the Velocity, Position and the Force acting on
each atom. I get the position of the group from the trjconv function using
the trajectory file (.xtc).
My questions are-
1. How can I get the velocity and force acting on each atom? ('using only
gromacs' is preferred)
< I know it's stored in the .trr file. Taking larger .trr file into MATLAB
causes too much RAM which I cannot afford. >
2. Is My way of determining the torque acting on the group correct? (I have
a very poor knowledge on Mechanics for atomic level calculations).
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