Questions tagged [namd]

For questions regarding NAMD (Nanoscale Molecular Dynamics), a software for molecular dynamics simulations.

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6 votes
1 answer
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Should I use a different cut-off scheme for non-bonded interactions when simulating a system with MD in vacuum?

I am currently doing a simulation of the behaviour of various sizes of water droplets (~100-1000 water molecules) in vacuum. I am using NAMD with the spherical boundary conditions to keep the droplet ...
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8 votes
1 answer
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How do I build and run a simulation of water molecules in NAMD?

So, I have started to learn NAMD because I need that for a project I will be doing in the next couple of months. I have some prior experience of MD with gromacs. I thought that since NAMD has a GUI ...
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