Hi,
I am currently using GROMOS 96 for simulation of molecules.I want to simulate my two designed peptide for a 100ns md run. What should be the optimum runtime for NVT and NPT minimization?
There is no set time frame. Equilibration should be carried out long enough such that the thermodynamic observables of interest in the ensemble converge.
I know that but is there any optimum or minimum condition for that ? e.g.- I am using 500 ps nvt and 1ns npt equilibration time for two 12mer peptide's 100ns md simulation. But it is not coming as I am expecting for this two molecule peptide simulation. The condition I am using is correct ? or I have to increase my time frame for nvt and npt eqilibruim, or I have to increase the MD run time frame.
What is happening that you aren't expecting? You need quantitative metrics to assess the progress of equilibration. The initial (usually restrained) equilibration should be assessed in terms of whether temperature, density, etc. are stable. If they are, then it's time to move to data collection (which also involves discarding some initial frames if the previous phases are restrained).
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