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2 votes

Controlling Initial Velocities in NVE Trajectory Simulations with VASP

As I understand in your question, you want to perform AIMD with NVE ensemble. Based on VASP documentation, it is recommened to set MDALGO=1 and ...
Jaafar Mehrez's user avatar
1 vote

My CHARMM IC table generation has caused hydrogen to bond to two carbons. How do I fix this?

I was able to build the structure correctly using the following input file ...
Hemanth Haridas's user avatar
2 votes

How to compute the Elastic Modulus of a molecule using GROMACS?

You can apply certain strains to the system by modifying the input structure, e.g. stretching one direction and fixing the other directions. After running MD, one can extract stress components. Keep ...
Lukas's user avatar
  • 121
3 votes

Velocity autocorrelation function for molecular dynamics trajectory

I think I managed to solve the problem. The code is now: ...
horlust's user avatar
  • 51
3 votes

What is the best way to optimize molecules with 8000 atoms. This includes C,H,O,N,Si

First, "best" is ill-defined. The best method would be full configuration interaction at the complete basis set limit including fully relativistic and quantum field theoretical corrections; ...
Susi Lehtola's user avatar
  • 18.4k
1 vote
Accepted

Geometry of H2O in the v=1 vibrational state for AIMD simulation

"Geometry" is complicated in quantum mechanics, because we have probability distributions rather than precise geometrical positions as we would have in classical mechanics. If we make the ...
Nike Dattani's user avatar
  • 34.6k
1 vote
Accepted

Equilibrating Surface Temperature Through NVT Ensemble Ab Initio Molecular Dynamics

"Ensemble" is a pretty strong word for a system with fewer atoms than the cards in a poker deck of cards. The Nose-Hoover thermostat attempts to redistribute energy between a system's ...
Shern Ren Tee's user avatar
6 votes
Accepted

Speed of atom from kinetic energy of molecule

What is the kinetic energy of a molecule? There is not just one type of kinetic energy when we have a composite system (made up of more than one particle, as in the case of a molecule). For example, ...
Nike Dattani's user avatar
  • 34.6k
1 vote

How to use martinize.py?

As per the README we can invoke martinize as follows: martinize.py -i input.pdb -o output.pdb I ran the command on a PDB of 4poj And I get the following output ...
Vandan Revanur's user avatar

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