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Questions tagged [molecular-mechanics]

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0answers
214 views

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 "...
2
votes
0answers
160 views

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 ...
2
votes
1answer
68 views

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 ...
2
votes
3answers
264 views

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 ...
6
votes
2answers
1k views

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 ...