All Questions
Tagged with namd molecular-dynamics
4 questions
5
votes
1
answer
76
views
How can I specify the direction of motion in the colvars file?
I am doing umbrella sampling in NAMD and I want to control the distance in the colvars to be in one direction. Is there any possibility?
- 1,652
2
votes
1
answer
46
views
How can a harmonic constraint be added between two groups in one direction using NAMD?
As a new user of NAMD, I am seeking assistance regarding a specific task. I intend to pull a LIGAND from outside to the center of a lipid using NAMD. To achieve this, I have utilized the colvar module ...
- 1,652
6
votes
1
answer
600
views
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 ...
- 7,171
8
votes
2
answers
2k
views
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 ...
- 7,171