Questions tagged [namd]
For questions regarding NAMD (Nanoscale Molecular Dynamics), a software for molecular dynamics simulations.
8 questions
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NAMD simulation NPT pressure fluctuation [duplicate]
I've made a simulation in NAMD in NPV.The pressure mean Is equal 1 but there Is a great fluctuation of values how can i fix It?
4
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2
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The performance of NAMD?
I'm interested in discussing the performance of the new version of NAMD. It seems that in this updated version, there's an increased reliance on GPU processing. However, despite using this new version,...
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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?
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2
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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 ...
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How to access Unit Cell Dimensions inside tclForces Script (NAMD)? [closed]
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.
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Restraining a specific bond in eABF simulations in NAMD? [closed]
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 ...
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6
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1
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600
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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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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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