How to change frames of MD simulation into times?

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

Need help in relating time scale of MD simulation with 'numstep' and 'timestep' values using NAMD

I wish to know the simple relationship between 'numstep' and simulation time. I mean, if I wish to run a one nanosecond simulation what should be the value that I should put in front of the numstep line of my configuration file? Secondly I want to know if the 'numstep' value is dependent on the 'timestep' value.

6 answers

Asked 16th Jun, 2014

Dr. Rohan Meshram

For example, if in my configuration file my timestep value is set to 1.0, then would setting the 'numstep' value to 1500000 suffice to yield a 1.5 Ns simulation?

In such a case if I change the timestep value to 2.0, is it necessary to double the numstep value to 3000000? I just want to be sure that by putting these values in a configuration file I am indeed doing the simulation on the desired time scale.

For convenience here is my configuration file details that I think is for 1.5 NS run. MD cons are humbly requested to see if I am doing it right.

#### input topology and initial structure ####

coordinates topo_equil010.coor # Reading the final structure from

structure ionized.psf

bincoordinates topo_restart_equil010.coor # equilibration stage in a binary format

#binvelocities protein_restart_equil010.vel # Initial velocities from restart file

###########################

#### force field block ####

###########################

paratypecharmm on

parameters par_all27_prot_na.prm

exclude scaled1-4

1-4scaling 1.0

dielectric 1.0

#### dealing with long-range interactions ####

#######################################################

rigidTolerance 0.00001

rigidIterations 100

#### this block specifies the Ewald electrostatics ####

#######################################################

PME on

PMETolerance 0.000001

PMEGridSizeX 96

PMEGridSizeY 120

PMEGridSizeZ 98

####################################################################

#### this block specifies the parameters for integrator and MTS ####

####################################################################

timestep 1.0

fullElectFrequency 4

####################################################################

######## this block determines the output ##########################

####################################################################

outputenergies 1000

outputtiming 1000

binaryoutput no

outputname topo_quench010 # The file name (without extension) to which final

# coordinates and velocities are to be saved

# (appended extensions are .coor or vel)

restartname topo_restart_quench010 # The file name (without extension), which holds

# the restart structure and velocities

# (appended extensions are *.coor or *.vel)

restartfreq 10000

binaryrestart yes

DCDfile topo_quench010.dcd # Trajectory filename (binary file)

dcdfreq 1500

####################################################################

####################### MD protocol block ##########################

####################################################################

seed 3010 # Random number seed used to generate initial

# Maxwell distribution of velocities

numsteps 1500000 # Number of integration steps during

# production simulations

temperature 300 # see also (b)

####################################################################

######## this block defines periodic boundary conditions ###########

####################################################################

cellBasisVector1 93.08 0.0 0.0

cellBasisVector2 0.0 118.56 0.0

cellBasisVector3 0.0 0.0 96.30

cellOrigin 35.17000961303711 -1.7790613174438477 -14.380327224731445

wrapWater on

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