I need to simulate nanofibrillated cellulose. For measuring hydrogen bond strength which molecular dynamic software is better. i.e. GROMACS, LAMMPS, Amber, NAMD?
There is NO good or bad MD simulation Software,it depends users perception ,if your new to this you can start with GROMACS their support is awesome
Yes, it depends on your chemical systerm and resources. All MD code are good. Yet, i would say Desmond is free and less time taking as per my experiance.
They are all free to my knowledge. There are some differences in their strengths and weaknesses. I'm mostly familiar with LAMMPS and GROMACS and would say that LAMMPS is very flexible and can thus be a suitable choice if you want very specific things with constrains, flows, or boundaries. GROMACS is a lot more computationally efficient, which is a huge advantage if you need to output for example hundreds of nanoseconds for a system with tens of thousands of atoms. Of course it depends a lot on your resources what it realistic.
Long story short, both codes are fine, and probably so are the other codes you suggested. For your decision I would consider a few things:
- Can people around you help you to get started with any of these packages
- How complicated or large are the simulations that you have in mind
- In what format are input files or forcefield parameters available or easy to generate. For example, many biological molecules are available in databases in a format that GROMACS is compatible with, while some conversion might be needed to use them with LAMMPS.
Thanks everyone for your response. @Remco Hartkamp those thing you can consider for a decision.
1. I will get very little support from the people around me. Actually our lab research topic more experimental than simulation.
2. In my simulation i have to handle quite big number of atom as i have to calculate strength of between nanocellululose fibers.
3. I only have to handle cellulose molecules.
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