I've done 2ns protein-ligand MD simulation in two ways
1. first I used general MD simulation, generating every single file by commands as suggested in gromacs tutorial. As an output, I've got 200 frames from 2ns MD simulation using tutorial .mdp files
2. secondly I generate parameters (.mdp) files using the charmm GUI web interface. and do the simulation in gromacs. this time I've got an output of only 20 frames from the same 2ns MD simulation.
My question is why is there a difference in the frames? am I missing something or do I've to change some parameters in the .mdp file?
please help
thank you
Sultan Khan
Assalam o alaikum wa rahmatullahi wa barkatuhu
Hope you doing well
In gromacs, the trajectories are made each 10us of simulations, and GUI command generates trajectories each 100us so it's not a big deal but its explanations should be explored.
Hi, there is keyword in mdp file that controls the frequency at which the frames in output files have to be written. You need to set that correctly. These keywords are like nstxout, nstvout, nstvout and other similar ones.
Here, in nstxout, x is for coordinates, f for forces, v for velocity etc.
For further details, please read the gromacs online manual.
Dear Sultan Khan
Open the .mdp file with a text editor, the total number of frames in the trajectory output file can be calculated by dividing the total number of simulation steps by the "nstxout-compressed" value. For instance, a system with a simulation runs of of 5,000,000 steps (nsteps = 5000000 [10 ns]) and a "nstxout-compressed" set to 5000 has 1000 frames (5000000/5000 = 1000)
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