Hi,
It doesn't. If the input trajectory doesn't have any velocities, there's no
way to compute any from e.g. forces, and in general they would not match
the original trajectory anyway.
On the original question, the alternative is to compute the displacement of
the COM over time and thus the
On 8/8/18 10:33 AM, ARNAB MUKHERJEE wrote:
Hi,
Thank you very much for your suggestion.
By "nsteps" I meant the # of step interval between which I would record the
velocity. So my simulation run has 10 million steps (200 ns) and I chose
nstvout = 1000.
But I was wondering is it possible to
Hi,
Thank you very much for your suggestion.
By "nsteps" I meant the # of step interval between which I would record the
velocity. So my simulation run has 10 million steps (200 ns) and I chose
nstvout = 1000.
But I was wondering is it possible to do a mdrun -rerun (changing the .mdp
file), and
On 8/7/18 1:47 PM, ARNAB MUKHERJEE wrote:
Dear all,
I have simulated a system of DNA and Protein, and I want to calculate the
velocity of the center of mass of protein as a function of time. So I used
the following command :
gmx traj -f traj_comp.trr -s md_run-E-Field.tpr -n index.ndx -ov
Dear all,
I have simulated a system of DNA and Protein, and I want to calculate the
velocity of the center of mass of protein as a function of time. So I used
the following command :
gmx traj -f traj_comp.trr -s md_run-E-Field.tpr -n index.ndx -ov
test-vel.xvg -com
I have pasted below the file
