Questions tagged [namd]

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

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How to access Unit Cell Dimensions inside tclForces Script (NAMD)?

I have a NAMD system with PBCs (FlexibleCell on) and I need to access the unit cell information to manually apply wrapping to some atoms in the system such that i may apply custom restraints to them. ...
AstraLoco's user avatar
2 votes
0 answers

Restraining a specific bond in eABF simulations in NAMD?

I am currently running eABF(adaptive biasing) simulation using NAMD. I need to restrain a few terminal C-H bonds in the system. I tried including the additional definition for bond constraints in the ...
Hemanth Haridas's user avatar
6 votes
1 answer

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 ...
S R Maiti's user avatar
  • 6,276
8 votes
2 answers

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 ...
S R Maiti's user avatar
  • 6,276