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Questions tagged [atomistic-simulation]

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What are some recent significant developments/studies in theoretical nonlinear chemical dynamics?

During my undergraduate studies, I was introduced to oscillatory and nonlinear reactions, which are essentially chemical reactions oscillating far away from equilibrium conditions - A very visual ...
mykd's user avatar
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7 votes
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How is temperature changes implemented in a molecular dynamics simulation?

I copied my question to this community as the advice of a user on Physics SE MD simulations are always associated with a temperature that represents the natural state of a system. However, some ...
Paul's user avatar
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4 votes
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Understanding use of Machine Learning in Multiscale Enhanced Sampling

Multiscale Enhanced Sampling Using Machine Learning Multiscale enhanced sampling (MSES) allows for enhanced sampling of all-atom protein structures by coupling with the accelerated dynamics of the ...
user366312's user avatar
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3 votes
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NPT Molecular dynamics calculation problem

I am trying to heat up my system from 10K to 300K using the NPT ensemble. But the temperature doesn't reach 300K. What do you think is the problem? This is my code for the heating part. However, the ...
anumoy ganguly's user avatar
3 votes
1 answer

Layer detection in a crystal structure

Context I have two images from a Monte Carlo Basin Hopping where silicon (in yellow) is getting replaced by germanium (in blue). Both have 32 germanium atoms at Si/Ge = 2.5; only the Ge distribution ...
Saha_1994's user avatar
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How to get started modeling liquid crystals?

I am an experimentalist who is interested in getting hands on experience with how simulations play into our understanding of liquid crystal formation. I have tried to read several reviews on the topic ...
Yetinsyny's user avatar
3 votes
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Perform energy minimization of multiple models of protein-dna complexes

Is there a software/standalone tool that can perform energy minimization of a large number of protein-dna complex models (more than 1000)? I know of GROMACS or Chimera or the online servers but is ...
Lily Sharpton's user avatar
2 votes
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Restraining a specific bond in eABF simulations in NAMD?

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 ...
Hemanth Haridas's user avatar
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simulate liquid solvent mobility through gel polymer electrolyte

I would like to simulate a liquid solvent (such as TEGDME) embedded into a polymeric cage (such as PEGDM). What is the most meaningful approach to estimate transport properties in such system? Is MD a ...
Marco Di Gennaro's user avatar