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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!
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As far as I understand, you are going a wrong way. MD simulations of polymers cannot give you any phase-diagram, and they are very computationally expensive.
You refer to field theoretic approach of Fredrickson and others, which is essentially a mean field approach, where you reach equilibrium density distributions molecular species via a self-consistent manner. Consequently, there is no molecular dynamics and you work with coarse-grained beads that represent the whole monomer instead of real atoms.
You may start with a bit of polymer physics, mean field approaches, and Flory-Huggins theory. The method is called the self-consistent field theory, which is essentially a classical density functional theory. I think you may have to write your own program for simulations. You may read one of my old papers, and the references there in
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Hi,
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!
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At small shear rate, you may have average over a long time to get a nice profile.
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Hi,
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?
Vidhya
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Thank you @Dr Ijaz
I will look into those papers.
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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?
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Hello Brian Adam,
I do not have an idea on your simulation configuration; however, I may suggest you modifying the neighbour lists to reduce the complexity of your simulation if you have not already. You may find more information about neighbour lists in LAMMPS manual. Even though this will not be critical as the neighbour lists, you may also consider decreasing the cutoff distances defined for the pairwise interactions.
Both of them are commonly used to decrease the complexity and the simulation length by giving up on some accuracy of the simulations; so, you need to be careful while assigning some values to them.
Regards
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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.
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Can you attach the entire code, and all input and output files?
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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.
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suspension (particles plus fluid), ...f denotes an average over the fluid phase only,
n is the particle number density and the average ‘hydrodynamic’ stresslet is defined as
a number average by SH = (1/N) ΣN
α = 1SH
α , where the stresslet of particle α is given
by
SHα = 12Sα(rσ · n + σ · nr) − 2κ − 23η(n · u)I − 2η(un + nu)dS; 
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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.
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I want to correct, the denominator in the equation 3 is "s" not "µ".
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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?
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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?
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Brownian dynamics is a simplified form of Langevin dynamics. Specifically, Brownian dynamics doesn't update the velocities of particles and only considers the changes of positions.