Greetings,
i have done an MDS of 100 ns (1000 frames) using NAMD and want to use the MMPBSA script in ambertools20. However, i dont know which interval should i write in the &general part of the input file.
should i use all of them (interval = 1)?
Often the interval is set to 10 ps. However, considering that you have 100 ns and 1000 frames, the minimum time inveral is 100 ps. Then you just use this interval and set the variable 'interval=1'. Note that 100 ns does not ensure convergence. You may run longer to check it.
Often the interval is set to 10 ps. However, considering that you have 100 ns and 1000 frames, the minimum time inveral is 100 ps. Then you just use this interval and set the variable 'interval=1'. Note that 100 ns does not ensure convergence. You may run longer to check it.
If you use interval 1 you will get slower calculation speed, if you skip the interval it may increase the speed of the calculations. It depends on what you are looking for, even for 10 ns you will get some output, and running longer run depends on the requirement of your MD system. In my opinion, give a try for different intervals and check the output energies, the one which is more converged is better as usable data.
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