I am performing molecular dynamics simulation using NAMD for a protein-protein complex.
The configuration files were generated by Charmm GUI.
Step4_equilibration.inp (at the end of the file):
minimize 10000
numsteps 90000000
run 125000
Step5_production.inp (at the end of the file):
# run
numsteps 500000; # run stops when this step is reached
run 500000; # 1ns
I want to run the MD for 100 ns. What should I edit in these files to make the run 100ns ??
Do I edit in both files ( equilibration and production files) or only the edit will be in the production file?
I hope this is what you were looking for. The edits can be made as per your choice in the input (.inp) files generated from CHARMM-GUI.
Equilibration configuration edits for running it for 1ns:
minimize 10000;
#numsteps 90000000;
run 500000 # 1ns equilibration
Production configuration edits for running it for 100ns:
#numsteps 50000000;
run 50000000 # 100ns
Yes, Thank you very much..
Another question if I may, how long it usually takes to run 100ns?
I tried using windows shell and it took over 30 hrs to reach 0.6ns, also tried colab and reached 1ns after 8 hrs but the session was interrupted after that..
Also how can you speed the run?
Makarim Osman The time depends on the spec of your PC/Laptop. I usually run it on an 8-core laptop with 4GB NVIDIA GTX 1650 graphics card with i5 11th generation processor and a run of 10ns takes me somewhere between 22-23 hours to complete. I don't run 100 ns at a stretch and break my simulations every 10 ns.
If you have a faster processor, it might take you lesser time to complete the simulation. Running on a dedicated GPU is always a bonus with NAMD. Based on your processors and availability of GPU, you can use the following command in your Windows PowerShell to activate the GPU use for running the simulation:
namd2 +idlepoll +p8 +devices 0 md_run.namd >md_run.log
Here +idlepoll command will help namd access the GPU, +p8 will denote it to use all 8-cores in addition to the GPU and +devices 0 is a command to run it all through only the device in use. You can substitute your config file .inp in place of .namd and run the command.
Hope this answer is useful to you.
Adhish Mazumder,
When you break your simulation for 10ns at a time, how can you resume starting from the previous end point?
Makarim Osman You can restart by editing the first timestep in your config file to the match the last time step of your previous run and then adding the following changes to your config file.
set inputname step5_production_10ns;
binCoordinates $inputname.restart.coor; # coordinates from last run (binary)
binVelocities $inputname.restart.vel; # velocities from last run (binary)
extendedSystem $inputname.restart.xsc; # cell dimensions from last run (binary)
where the input name should match your last run output name.
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