New answers tagged molecular-dynamics
3
There are many deficiencies in pairwise force fields that are balancing to perform well at some specific task. Pairwise interactive force fields are almost always parameterized to reproduce some kind of experimental data. That experimental data is gathered at some finite temperature and pressure and most likely does not appear in the actual potential. That ...
4
Pairwise force-fields neglects 3 body and higher interactions (many body). As Nike pointed out, there are force-fields that can take into account higher order interactions and still be somewhat pairwise, but parameterizing them is hard(er). It is easier to parameterize a simple model, and often, more accurate. We have put alot of work into simple pairwise FF'...
7
The Axilrod-Teller force is not a "pairwise" force but a "3-body" force whose potential has the formula:
$$\tag{1}
V_{ijk}= E_{0} \left(
\frac{1 + 3 \cos\gamma_{i} \cos\gamma_{j} \cos\gamma_{k}}{\left( r_{ij} r_{jk} r_{ik} \right)^3}
\right),
$$
as opposed to a pairwise force like the Van der Waals force which is commonly used in ...
2
This was answered on the matsci LAMMPS forum by Axel Kohlmeyer.
To summarize, there is a known bug (still unresolved as of 7/28/2021) that leads to a corrupted neighbor list when using GPUs in combination with a hybrid pair style. Axel suggests using the command lmp -sf gpu -pk gpu 1 neigh no -in in as a workaround.
3
There are a number of open-source and commercial software that can do a completely random substitution alloy.
In the open-source segment, you can try the python software: Pymatgen (https://pymatgen.org/). Atomsk (https://atomsk.univ-lille.fr/) is another great software to do this. I have tried to do this using Atomsk and it works perfectly.
In the commercial ...
7
Any parameters are better than no parameters. Part of using a FF is checking that results make sense, so if you can find something in this bare market for anions, try it. Proof will be in the pudding.
LigParGen can only generate ions between -2 and +2 charge, so $\ce{PO4^3-}$ is out. When I tried with $\ce{SO4^2-}$, it did not work. $\ce{H2SO4}$ also did not ...
7
The flying ice cube effect is when the kinetic energy leaks into the translations and rotations.
In a constant energy simulation (NVE) this must come at the expense of vibrations, which has the effect of "freezing" the bonds, angles and torsions. Obviously, this is a purely classical effect because even at 0 K a bond will vibrate at the zero-point ...
10
High frequency in this case is 'particles move all independently, with different directions and speed', and low frequency means 'particles can be represented as gradually changing field of speed and direction of particles in the region'. Something like 'frequency in space', how often to change speed and direction as you observe more and more particles.
If ...
7
Replica Exchange
Methods like temperature replica exchange and Hamiltonian replica exchange can help to sample phase space more uniformly. For temperature replica exchange, we have the base temperature that we are interested in (often room temperature or body temperature) and a number of other replicas with higher temperatures. For instance, we could have 10 ...
6
I wasn't going to answer, because there is no answer, but, anyways...
First: common practice is...
Common practice is to frequently measure the property you are after, as well as others, such as internal energy, density and make a plot. The property will fluctuate but eventually reach an equilibrium that is easy for the eye to spot on a plot. Or, use the ...
10
Since you seem to have at least a start on automating the process of modifying the file, I will just address the other two parts of your question: the format of the nonbond_params section of a GROMACS .itp file and the meaning of the symbols used in the Martini force field.
GROMACS format
This is given in the GROMACS manual. To summarize:
Atom1 Atom2 Func ...
7
I believe I have figured it out.
For those trying to martinize their all-atom files into coarse grain representations for martini 3, use the following package:
https://github.com/marrink-lab/vermouth-martinize
With respect to modifying the water for IDP simulations, I pulled out the W, SW and TW interactions from the martini v3.0.0 forcefield, like so:
W ...
10
On the mathematical side, there exists no algorithm that estimates the time required to converge a property within any predefined accuracy, however low the accuracy is. The reason is simple. Suppose you perform a series of simulations of a liquid, with successively low temperature. When you are above the freezing point of the liquid, your simulation probably ...
10
tl;dr: simulate for greater than N*period of oscillation
To understand how I arrived at this answer consider that properties can be written as a function of the partition function Q.
For example, the average value of the volume will be
${\displaystyle \langle V\rangle =\pm {\frac {\partial \ln Q}{\partial \beta P}}.}$
The partition function for N identical ...
7
Generally, if you want to perform simulations with some force field, you will have to search the literature for published FFs tailored for your problem. The Stillinger-Weber (SW) model is very popular to describe bulk (diamond) silicon, for which it was designed in the first place. But several reparametrizations have also been published. If you happen to ...
5
Generally not. The pH difference between the two sides of a membrane can be very noticeable, for example when the membrane is that of a mitochondrion. Actually mitochondria works by actively transporting protons from one side of the membrane to the other side, using the chemical energy released by reducing O2 to H2O, and then use the proton gradient to ...
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