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Within statistical mechanics (SM) a molecular property $X$ is computed by $$\left<{X}\right>_{SM}=\sum^{states}_i X_i p_i$$where $X_i$ is the value of $X$ for energy state $i$ and $p_i$ is the probability of being in energy state $i$ with energy $E_i$:$$p_i=\frac{e^{-E_i/kT}}{\sum_i e^{-E_i/kT}}$$Within molecular dynamics (MD) the corresponding ...


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tl,dr: Forces are equivalent to the negative of the gradient, use small, arbitrary $\mathrm{d}r$ for each atom The problem, as you mention, with many neural network methods in chemistry at the moment, is that the $E = f(x,y,z)$ is a black box and thus analytical gradients (and thus forces) are often not available. First, as you clearly know, $F = -\nabla E(...


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This is intrinsic to Ewald summation methods, not software implementations. The uniform charge arises from neglect of a reciprocal sum term. It does not directly affect the dynamics and may be a reasonable model of a spatially homogeneous system. See https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-October/101544.html for further details and ...


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This question is actually very broad as the answer can change quite a bit based on what kind of thing you are doing with your MD simulation. The first thing to note is that the Boltzmann distribution only applies at thermal equilibrium. So if you start an MD simulation from a non-equilibrium state and then try to calculate the average of some property as ...


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#!/usr/bin/env python2 import MDAnalysis # file formats are automatically deduced; this is a standard topology and binary # (NetCDF) trajectory from AMBER topology = 'peptide_1.prmtop' trajectory = '02_peptide_1_equil_NVT.nc' u = MDAnalysis.Universe(topology, trajectory) with MDAnalysis.Writer("all.pdb", multiframe=True) as pdb: for ts in u.trajectory:...


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Another reason why people don't bother to use 310K versus 300K is because any time you are using MD, you have an approximate force field describing the dynamics of the system which means you have an approximate phase diagram for the system. When comparing MD and experiment, it is a reasonable question if you really want to compare properties at the same ...


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More a set of queries and comments than an answer. I don't understand why you make A and B vary with time irrespective of your reaction scheme. You should really analyse using Fick's diffusion equations with the reaction scheme added and do so for each species. This will have to be a numerical calculation in space and time. (There are well established ...


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Let us start by defining all the terms in Eq. 1 carefully, as the OP does not do so. I have always found it easier to interpret such models in the context of particles flowing from state to state, and that is the picture that I will try to present here. $T_{ij}$ measures the probability of going from state $i$ to state $j$ within a time $\tau$. $\pi_i$ is ...


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Is it true that an evaporating molecule has the same kinetic energy as a molecule in a pot of boiling water? Well for one the kinetic energy for a given temperature is an average kinetic energy of a distribution of energis. So for the question: "Is it true that an evaporating molecule has the same kinetic energy as a molecule in a pot of boiling water?" ...


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Seems true just by the definition of boiling point. At boiling point your liquid is in equilibrium between its liquid and gas phases, hence the "average" molecule will possess that minimum amount of kinetic energy to escape into the gas phase (and vica versa the maximum for it to condense back into the liquid phase). In your earlier example, at "room ...


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This depends on the organism you are studying. I work with Bac and human, I have simulations running at 300k and 310k. Search on the organism you are going to work on and adjust its temperament for your simulation.


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First, whether you use DFT or molecular mechanics to get your energies and forces doesn't really matter. If you have equations of motion, forces, and energies then you have the dynamics necessary to sample an ensemble and from there you should be able to get any physical observable you desire. It is often very difficult to determine free energy changes ...


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You want to be able to compare your simulation with the real world, and that means you do (or look at other's) in vitro experiments, which are predominantly (at least for starters) done at room temperature because that's simplest. Further you want to be able to compare to results of earlier simulations (other MD engine, varied chemical system), and you want ...


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1 - "Force Field" (FF) means the set of equations that describe the interactions between atoms and the set of numerical parameters that people using those particular functions have come up with to describe some molecules (typically proteins, Nucleic Acids, lipids, and a few others). Many FFs exist because of different choices in functional forms, in the ...


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Let us first note that the calculation of the first derivative of the total DFT or HF ground state energy of a molecule with respect to its nuclear coordinates (called the gradient) depends on a converged self-consistent field (SCF) solution. The solution is obtained in an iterative fashion and is represented as a collection of molecular orbital (MO) ...


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At the top of your config file, you imply that you want to perform an NVE calculation, but you’re actually doing NVT, because you have the Langevin thermostat turned on. Langevin works by giving the system a random “kick”, which is probably spiking the energy.


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This is possible with the Python package MDTraj. Assuming you have your trajectory saved as trajectory.dcd and topology in topology.pdb: import mdtraj as md from mdtraj.geometry.alignment import compute_average_structure traj = md.load('trajectory.dcd', top='topology.pdb') average = compute_average_structure(traj.xyz) I believe it will RMSD align the ...


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The application of periodic boundary condition does not mean that the system is explicitly replicated. You only deal with the particles within the unit cell (the box that you replicate), but you let them interact with the replicated ones outside of this unit cell. Consider a simple 1-dimensional case with three atoms in the unit cell: $\ce{A-B-C}$, and lets ...


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A battery has a small shelf life if it discharges internally. Saying that a discharged battery is in chemical equillibrium (or much closer to it than a fresh one) is a true statement, obviously, but nothing else. If you reverse the polarity of a primary battery, you get some other reaction than the one happening during discharging backwards. That says ...


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Thank you, Buck, for all your suggestions. You're right that a good way to check the influence of the volume is to try varying it. I did that by using the maximum and minimum volumes of the fluctuations in one simulation. There was some variation, so the volume does matter! I was lucky enough to hear about "travis," an amazingly simple-to-compile code (...


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I haven't done it in vmd, but a rdf is really kind of like a histogram. For a particle of interest, you count how many particles are between r and $\Delta r$ from it and record that number in a bin, then move outwards, recording numbers in each shell into a bin for that shell. That tells you the rdf of that particle interacting with everything else. If there ...


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Someday I was wondering as you are doing but I think that now my confusion has lessened considerably after talking with experts in the field and enrolling in a master program of pharmaceutical chemistry and drug design. Different kinds of simulations can be called modelling of cellular processes. The first are the rules of systems biology and the ...


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First of All thanks for your answer Erdem Caner. After your answer I found VFFDT download link and I created my *.frcmod file with this program. Here is the VFFDT link: https://www.dropbox.com/sh/hlefz8xy8o23q44/AADZGTBN-aJ07flZ-kM0s4U6a?dl=0 After download the program be careful your OS language must be English. Then run program according to manual which is ...


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I really don't know exact answer but I have an idea for you it may help: You can use some "force field developer toolkits". One of them is: VFFDT. It parametrizes (for amber forcefield *.frmcd files) bond and angle force constant from gaussian out/log file.


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I ended up realizing that if you run: parm prmtop-file trajin netcdf-file vector v0 :1-4@heavy-atoms-from-molecule-1 :5-8@heavy-atoms-from-molecule-2 out v0.out magnitude run quit You will get the total distance as well as x, y and z distances between your two molecules. The output file will contain 8 columns. The AMBER manual states that they are ...


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