Question
Asked 6th Jul, 2020

How to change frames of MD simulation into times?

I want to draw a graph of the salt bridge against time but I have frames instead of time so I want to know how to convert frames into time (µs)?

Most recent answer

All Answers (5)

8th Jul, 2020
Mohammad Saeed Bahramy
The University of Manchester
If you know the time step used in your MD simulation, you can multiply it to your frame number to get the actual time.
8th Jul, 2020
Martin Klvana
t = N * dt, where N is number of timesteps and dt is timestep.
Example: Frames (1, 2, 3, . . .) are stored every N=1000 timesteps.
t1 = N * dt; t2 = 2 * N * dt; t3 = 3 * N * dt, . . .
1 Recommendation
8th Jul, 2020
Inna Ermilova
Chalmers University of Technology
Hi Hafiz! You shall check your output options in your mdp files and the time-step. Then you shall multiply the time-step with the number of frames in the output option. On the other hand you can use VMD software for calculating the salt bridges, but there you will also have to use the knowledge about your output options from mdp-file.
1 Recommendation
9th Jul, 2020
Muhammad Ikhlas Abdjan
Airlangga University
I beg you pardon.
You can change your input file for each stage (min, heat, equilibrium, and production)
I do calculation for production stage (20 ns) like below:
Frames=Nstlim/ntwx
Frames=20000000/5000
Frames=4000
#MDS Time
MDS time= Nstlim*dt
MDS time= 20000000*0.001
MDS time=20000 ps = 20 ns
#Convert from frames to time
=Frames/MDS time
=4000/20 ns
=200
=200/Frame
I hope that helps

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