hello, I have a query. I am running 50ns md simulation on GROMACS. I have used CHARMM-GUI for initial file preparation… After that i used following commands for md run
gmx grompp -f mdout.mdp -c step4.1_equilibration.gro -t step4.1_equilibration.cpt -p topol.top -n index.ndx -o md_0_50.tpr
gmx mdrun -v -deffnm md_0_50
In RUN CONTROL PARAMETERS dt= 0.001 nsteps= 125000 why this is so???
because we have studied in MD Simulation during my course of MD Simulation that for 1ns = 1000ps = 500000 nsteps but here when i run the simulation of 50ns why nsteps are showing as (nsteps=125000 125.0ps) on my console?? why calculation is different. Is there any error in my command?
Looks like you are using the wrong mdp file after the -f flag.
It should be called step5_production.mdp or something like that.
You are preparing the binary for the new simulation (md_0_50.tpr) with the mdout.mdp output file that is generally generated by GROMACS after the grompp preprocessing. Please read the README in the directory you downloaded from CHARMM-GUI to look for the correct loop implementation that will run all your sims as supposed
Hi Saima! I suspect that in your course the time step, dt, was 2 fs which was written as dt=0.002. Now your dt is 0.001 which is 1 fs. That is why you don't see what you expect. Gromacs reads dt in ps. Then in order to know the time you multiply the time step with the total number of steps and you will get the value in ps. Also check out you output parameters for trajectory, i. e. how often you record it in xtc or try files, because this will also have an effect on the accuracy of your final results.
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