I am new to NAMD and recently run a simulation of DNA-organic molecule interactions in NAMD for 20 ns. I want to know what the different results are that I should analyze using the output of the simulation, and what about the interaction among these molecules and other graphs and results?
What you should ask yourself is - why did you conduct the simulation? What hypothesis were you testing? That should steer you towards the analysis techniques you need to address a scientifically interesting question. Analysis is part of experimental design; it should be planned before you even start the simulation, as it will also help you determine how to do the simulation and how long it should run.
What you should ask yourself is - why did you conduct the simulation? What hypothesis were you testing? That should steer you towards the analysis techniques you need to address a scientifically interesting question. Analysis is part of experimental design; it should be planned before you even start the simulation, as it will also help you determine how to do the simulation and how long it should run.
Thankyou for the reply, I just want to understand how to analyse whether the simulation result is correct or not, what are the important analysis to be required to understand that the output is correct. I understand that the experimental work is required to make the appropriate comparasion, but, for MDS what could be important results and analysis are mandatory.
What do you mean by "correct?" Do you mean that you want to verify whether the simulation is reliable, or whether it correctly reproduces some experimental outcome? And again, there is no such thing as a "mandatory" analysis. There is no one-size-fits-all approach here.
The most important thing, since you are new to NAMD, is to check that you set up your simulation correctly: double check water density and total charge of the system (should be zero), make sure that you used good grid spacing for PME (around 1 Angstrom), good parameters (Charmm 27 or 36 with NBFIX for ions), reasonable cutoff scheme. Actual analysis depends on the reason behind running that simulation. For example, you can get the number of hydrogen bonds formed. I'm pretty sure that suggestions can be more specific if you provide more details.
Side note: this question should have been probably tagged with VMD as well, since this is the program that let's you do a lot of analysis fast.
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