Questions tagged [molecular-mechanics]
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Starting configuration for Molecular Dynamics
I have to build a bilayer using a structure obtained in a previous MD simulation. In the structure, some chains of the molecules cross the simulation box as shown below. I added water layers to the ...
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Comparison of computational complexities of MD versus MC simulations
In my humble understanding MD simulations of systems with short-range(like LJ interactions) and long-range(electrostatic) has a computational complexity $O(N . log(N))$. What will be the computational ...
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minimalistic library for classical molecular mechanics force-field in C/C++/Python
I would like some classical molecular mechanics forcefield library or super-simple program which does not have any external dependences, so that I can plug it into my software without worry of "...
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temperature set point maintenance with Langevin thermostat + shake algorithm
During the past ~4.5 years of my PhD, I have written an MD code, based largely on LAMMPS and NAMD, however reparallelized to suit my computational scenario better. One important thing to mention ...
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Is it common or to use objects for calculation of pair interactions in physics and chemistry simulations?
When simulation atoms, molecules, colloids, autc., are there programs that define each interacting unity as an object in the OOP sense?
In my own case, I've been simulating magnetic nanoparticles in ...
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Side chain rotamers sampling in protein
What is the best tool to sample rotamers in side chain amino acids in a protein? More exactly, I want to sample the different rotamers only for lysine residues while keeping backbone rigid. I've tried ...
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Minimum image convention for triclinic unit cell
The minimum image convention (MIC), see for example a short note of W. Smith, is often used in molecular dynamics or monte carlo simulations of periodic systems with an orthorhombic unit cell. For ...
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