# Tag Info

14

No, that is not possible. What is possible is to estimate how much more time you need to calculate the electronic energy if you increase the system size by some factor. For any method which uses LCAO-MO expansion, it is the number of basis functions $m$ which primarily determines the computational cost, so that it is usually used as a measure of the system ...

8

I reproduced your calculations with PBE/def2-SVP (using Orca). The energy "jump" is even smaller than with MP2, however the causes are probably the same. So here is my answer: The planar structure is a Transition State, with one negative frequency. The dihedral you are scanning is probably not the best to describe this twisting. Now in more detail. Here ...

7

This has nothing to do with box walls (there are no walls!) or restraining the waters. You do not want to do that! Do not confuse periodic boundary conditions with wrapping to the central cell. Look at the amber tutorials, it is all explained there. You either need to set iwrap=1 in your amber minor put your trajectory trough cpptraj and use autoimage. ...

6

Since it's been a couple of days, I guess I convert my comment into an answer. MMFF94s is Merck Molecular Force Field. From what I understand, the issue is that this FF has certain limitations when it comes to electrostatic interaction, estimating polarizability and intramolecular interactions, which confuses the method trying to predict 3D conformers for ...

6

Depending on the geometry of the hydrogen on the "imine" moiety of the guanadine, you could be creating a very strong syn-pentane interaction. In either case, either the lone pair or the hydrogen is being quite sterically crowded with with N-H's on the 5-membered ring. The planar form of this species actually looks pretty bad. I would expect a bit of out ...

5

Atomic units are the standard in almost any ab-initio (LAMMPS, NWChem, Orca, QChem) and/or classical force field (LAMMPS, MPMC, CHARMM, AMBER, GROMACS etc.) modeling code because you end up computing numbers much closer to 1. Things can get bad very quickly for small values in python. To prevent this, I would use atomic units, and wherever arithmetic error ...

5

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 ...

5

Have you considered a free-energy calculation? That is, calculate the free-energy of the dissociated species and of the neutral one, and calculate the pKa via the formula for activity. There was this GROMACS tutorial, but it seems the link is broken.

5

The modelling of metals using a 'simple' potential is relatively difficult. I have a suggestion for a force field, though it does not fit exactly all your criteria, but I would like to offer it anyway. Adri van Duin has developed a force field called ReaxFF. This force field is non-proprietary and is readily available in the open-source package LAMMPS. This ...

5

Most classical molecular force fields are parameterized for a set of elements and atom types. The MMFF94 method was designed for standard organic drug-like small molecules, so it has a limited set of elements (H, Li, C, N, O, F, Na, Mg, Si, P, S, Cl, K, Ca, Fe, Cu, Zn, Br, I) categorized into 99 atom types (e.g. mmffprop.par from the Open Babel ...

4

I guess for starters, try finding a torsion angle on a 3 point molecule. Is it fast enough, accurate enough? The real issue is why do some force-fields have intra-molecular bonds and others do not. Including bond and angle forces in water models make their computation more expensive. There are classes of flexible forcefields for water. There are even more ...

4

Your provided note is about the HF Hamiltonian in the one-electron basis set (atomic orbitals). Since a minimal STO-3G basis set is used here, the corresponding matrix representation of this Hamiltonian is a $2\times 2$ matrix. The $3\times 3$ Hamiltonian from the SI is the FCI Hamiltonian in the many-electron basis set. These basis functions are ...

4

#!/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:...

3

I'm basing my answer on T. Gould, T. Bucko, J. Chem, Theory Comput. 2016, 12, 3603-3613. In your TDDFT calculation, what you want to compute is the frequency-dependent dipole polarizability, $\alpha_{X/Y}(i\omega)$, that determines the dispersion coefficient, $C_6$. $$C_{6,XY} = \frac{3}{\pi}\int d\omega \alpha_X(i\omega)\alpha_Y(i\omega)$$ They also ...

3

Looks fine. 2. I'd phrase that more generally as the simulation volume would tend to expand. 3. But can only do so if the ensemble permits it (pressure can be negative in NVT). The fluctuations are a consequence of making an observation of a macroscopic quantity over small numbers of degrees of freedom, or time. See http://www.gromacs.org/Documentation/...

3

For some methods it would be theoretically possible to estimate the total time required to perform them, because they requires some specific steps (system dependents or not) for which the number of operations involved can be estimated. Knowing that and a measure of speed of the computer used for that mater (see for example: FLOPS) you can in principle to ...

3

You could have a look at VALBOND from Clark Landis, don't know how generally it was parameterized. LFMM from Rob Deeth is very good, but not many metals. I think old PCModel is still around, one of the better for metals. Allinger did a metal extension in MM3(94), with generalized parameters for the periodic table, but not much used. I've created a number of ...

2

There are multiple ways in which the VACF, along with other properties derived from molecular dynamics trajectories like the dipole ACF to give IR spectra, can be considered "converged". The molecular dynamics trajectory itself must be converged by some time-dependent statistical metric, such as measuring fluctuations in the energy or temperature over a ...

2

If i underatabd correctly, Now a days when in molecular dybamics simulation or docking studies, to calculate everything requires precise knowledge of polar, hydrophobic, ionic and non-bonding interactions. We have models to deal with each, and each has limitations. With polar groups the issues are not so much the models, which have distance dependance and ...

2

With the simple molecules in your system, using the Gibbs Ensemble Monte Carlo would be the way to go. Each phase gets its own simulation box, and particles are swapped back and forth until equilibrium is reached. Cassandra, DL_MONTE and other programs can do this easily for you. Once equilibrium is reached you can sample each box in the NVT or NPT ensemble ...

2

An artificial jump like this usually points to convergence issues. You could try reading the wavefunction from the previous step to converge to nearly the same SCF solution. If it is not that then it could have to do with how the geometries are obtained. You might want to read the previous wavefunction and tweak the geometry converger to take smaller steps ...

1

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 ...

1

The process of making structural models of macromolecules (the content of PDB files) is called model building, rather than generating, because it normally involves tedious manual building of the model in a graphical program such as Coot. A few programs can do automatic model building, but then the structure needs to be finished manually. Maybe this will ...

1

It's certainly more of a "back of the envelope" calculation than a rigorous proof. The main point is, that for a certain system, the cost of obtaining a set of trajectories with a given statistical accuracy is fixed with ab initio MD, as only the dynamically relevant parts of the PES are calculated. With what is here called "classical MD" (but also applies ...

1

It's hard/impossible to pinpoint the reason for your problems without seeing the code and knowing which terms you use. If you feel like sharing it, then you should probably head over to Computational Science and make a post there. A few general things come to mind: Check that you have $\sigma$ and $\epsilon$ values inserted in the correct order. Check the ...

1

First, when it comes to periodic boundary conditions, you should make sure that your system does not interact with itself through the boundaries. A way to check it is to see if the electron density is low in vacuum (in case your system has some void separating surfaces). Energies should also be checked to be converged with respect to cutoff energies, $k$ ...

1

This very much depends on whether you're trying to calculate the total energy, or whether you want to know the relative stability of different structures. The most convenient choice would be akin to Lennard-Jones dimensionless units (https://en.wikipedia.org/wiki/Lennard-Jones_potential#Dimensionless_.28reduced.29_units), if you're using a relatively simple ...

1

Free energies are computed by transforming one state into another, e.g. by transforming ligand A into a ligand B (inside a protein in our case). This transformation yields the difference in binding free energies between ligands A and B: $\Delta \Delta G^{bind}_{A \rightarrow B}$. This is a relative binding free energy. On the other hand, if ligand A is ...

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