Hi all
This is a question in this context is to reach conclusions.
If you have experience in the field of molecular dynamics with the software, please answer this question, what analysis you have done? And what is your experience of general software did you use?
thank you all
I don't think there is a generally applicable answer. You will hardly find any conclusion.
The properties of interest are largely system specific. It is definitely part of desired "scientific skills" to decide, what is important to measure/calculate. When running MD of a homogeneous liquid, density might be of interest, while in case of protein-ligand interactions, calculation of density could not contribute to better understanding of the phenomenon.
Each software package usually provides a toolbox for basic analysis (e.g. Amber ptraj or Gromacs "g_" utilities). One is expected to acquire some scripting/programming skills to calculate the system specific (thus interesting) properties (using e.g. python, R, matlab, bash/awk languages).
I don't think there is a generally applicable answer. You will hardly find any conclusion.
The properties of interest are largely system specific. It is definitely part of desired "scientific skills" to decide, what is important to measure/calculate. When running MD of a homogeneous liquid, density might be of interest, while in case of protein-ligand interactions, calculation of density could not contribute to better understanding of the phenomenon.
Each software package usually provides a toolbox for basic analysis (e.g. Amber ptraj or Gromacs "g_" utilities). One is expected to acquire some scripting/programming skills to calculate the system specific (thus interesting) properties (using e.g. python, R, matlab, bash/awk languages).
You have to understand the research problem, expected results. The software is a tool for testing hypotheses and understanding of the processes at the atomic level
After performing molecular dynamics, the properties to measure during your post-analysis is, as others have mentioned, dependent on the hypothesis or research question that you have in mind. For example, if you are investigating which part of the protein structure is rigid or flexible, you can analyze the root mean square fluctuation (RMSF) of all residues. Moreover, if you would like to know which residues are involved in protein-ligand interaction, you could compare the RMSFs of the ligand-bound and -unbound form of the protein structures and residues that displays changes to the RMSF are likely to be perturbed owing to ligand interaction.
And as Michal had mentioned, all MD software will provide a post-analysis toolbox for you to extract key properties after the simulation had completed. For ideas on the type of properties that you can extract from MD simulation, see the below link.
http://www.ks.uiuc.edu/Research/MMTools/
For the first model generation, Materials Studio is an excellent software. After model generation lammps is good to run the model.
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