Langevin Dynamics - Science topic
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A little background: I am an undergraduate student, a biochemistry major with little to no background in bioinformatics. We're only allowed to choose dry lab topics for our thesis since we cannot go to school to perform experiments in the chem lab.
I am currently very, very lost regarding on what to do with my thesis entitled: PHASE DIAGRAM FOR PHASE SEPARATION OF POLY(METHYL METHACRYLATE) COPOLYMERS USING FIELD-THEORETIC SIMULATION. I have been following works by Mr. Fredrickson and colleagues but they are difficult for me to understand.
My progress so far is that I've ran the Gromacs input files I've made in CHARMM Polymer Builder in SLURM HPC (these input files vary in solvents so that I could investigate the effect of addition of solvent to the phase separation). Now, as you can read in my title, I have to construct phase diagrams. Any help on how to construct phase diagrams (through FTS)? Thank you so much!
We are trying to simulate particles with Langevin dynamics in a shear flow by Lees-Edwards boundary conditions in MD simulations.
It seems thermal forces and shear flow do not go hand in hand, one example is given here:
In Lees-Edwards, the averaged velocity profile must be linear, however, with Langevin we get significant deviations from the linear velocity profile, even after we make a lot of averaging.
Is there a remedy to reconcile Langevin dynamics with Lees-Edwards boundary conditions in a MD simulation?
In advance, I appreciate your kind help!
I am doing Langevin dynamics simulation for a small system of peptides in explicit solvent.
I have performed NVT and NPT equilibration using normal MD simulation (md integrator) to allow the system get close to the experimental density. I obtained the average box volume of the system from NPT equilibration. I wanted to use this box volume to carry out NVT using Langevin.
Can somehow tell me how I can specify the box volume or box density during production run?
I'm running simulations for a bead-spring polymer networks using LAMMPS. I need my simulations to reach biologically relevant timescales of at least a few milliseconds. However each simulation would take upwards of a few weeks given my current use of Langevin dynamics and velocity verlet integration. I need to collect data on at least 50 such simulations, so this is prohibitive. Is there any way to improve performance? Are there absolutely stable, implicit integration schemes for molecular dynamics integrators?
I am trying to implement a FORTRAN code that can perform NVT simulation using Langevin Dynamics. I have been following the textbook by Allen and Tillesdly for the initial implementation of the code. I took the implementation details for the langevin dynamics from http://localscf.com/localscf.com/LangevinDynamics.aspx.html. I was able to generate random forces and random velocities using Box-Muller transform (thus a normal distribution). But the temperature from the simulation quickly overshoots the 100K that was set as the bath temperature. Any help on this would be very much appreciated. I am trying to perform simulations on liquid argon system.
I am using Stokesian dynamics to investigate the rheology of colloidal suspensions, I am calculating the stresslet in order to calculate the viscosity of the suspension. Since the sresslet is a 5 dimensional traceless tensor , do I have to calculate the average value of the components of the streeslet for each particle , in order to find the overall stresslet of the suspension.
I am trying to calculate size by fitting M vs H curve using langevin function, I know the langevin equation, but my query is we plot a curve between M/Ms vs H or meu.H/K.T? After fitting the curve with langevin equation how we get the parameters meu and Ms.
In usual MD simulations, we use a collision frequency of 1/ps. However, when studying properties like protein/RNA folding (without increasing the temperature) using sampling schemes like self-guided langevin dynamics; what should be the optimum value of this frequency? Should it set higher or lower than 1/ps?
Hi, does anybody know the difference between Brownian dynamics and Langevin dynamics methods? I read various articles but authors usually talk about Brownian or Langevin dynamics separately and don't compare them. I wonder if there is a scientific article (not Wikipedia) with such a comparison?