Questions tagged [molecular-modeling]

Questions to do with molecular modeling.

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Modelling Pd(111) and Pd(100) Surface Oxides Through VESTA

I want to build unit cells for Pd surface oxide models, but I am not sure how to begin as I am new to using VESTA. On Pd(100), the most stable surface oxide structure is √5x√5 R27o. On Pd(111), the ...
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4 votes
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66 views

Understanding use of Machine Learning in Multiscale Enhanced Sampling

Multiscale Enhanced Sampling Using Machine Learning Multiscale enhanced sampling (MSES) allows for enhanced sampling of all-atom protein structures by coupling with the accelerated dynamics of the ...
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2 votes
1 answer
47 views

What does it mean by a "site" in the case of a CG model?

A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions What does it mean by a "site" in the case of a coarse-grained (CG)...
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3 votes
3 answers
655 views

Is it correct to say "in molecular dynamics we are faced with..." or should it be "in molecular modeling we are faced with"?

In the paper "DeePCG: Constructing coarse-grained models via deep neural networks", it says: "In molecular dynamics (MD), we are often faced with two types of coarse-graining tasks. In ...
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2 votes
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Can protein modeling and simulation be used in developing a marketable product?

As we all know computer science, electrical engineering, etc. knowledge can be used in developing software and electronics/electrical products that can be sold to end-users (B2C). Can protein modeling ...
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5 votes
1 answer
115 views

Definition of the terms "modeling" and "simulation" in the context of biomolecules and/or proteins

What are the definitions of the terms "modeling" and "simulation" in the context of biomolecules and/or proteins? Examples will be highly appreciated. Also, please, back them up ...
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1 vote
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Interlink among different length scales of simulation and modelling techniques

I found this figure: In the following paper: A Review on Multiscale Modelling and Simulation for Polymer Nanocomposites However, I am skeptical about its correctness, as this paper is not peer-...
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3 votes
0 answers
36 views

Is the energy due to external electric field included in gromacs energy?

I have a Gromacs NVT simulation with a constant external electric field using the option "electric-field-z = 1.5 0 0 0". When calling gmx energy -f (...).edr to calculate the potential ...
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How much does it cost (RAM and CPU) to calculate the energy of H2?

I have recently come across this very intriguing paper “The Fundamental Vibration of Molecular Hydrogen”. I have asked the authors the following naïve questions directly via email: What was the ...
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4 votes
0 answers
64 views

Why can't DFT calculate the energy of magnetic diatomic molecules accurately?

I am trying to calculate the reaction enthalpy change of $\ce{2H2 + O2->2H2O}$, my plan is to calculate the energy of $\ce{H2, O2 \text{and} H2O}$, respectively, then do the simple math. But I find ...
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15 votes
5 answers
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What's the point of doing high accuracy spectroscopy calculations?

I am currently reading Dickenson et al. (2013) The Fundamental Vibration of Molecular Hydrogen. I am trying to understand why this calculation is important for the field beyond basic scientific ...
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2 votes
1 answer
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What is the relationship between periodic boundary and the simulation box?

Suppose, the size of my simulation box is: Width = 200 Height = 100 Where, Top-left corner = (0, 0) Bottom-right corner = (200,100) Center of the coordinate is at (100, 50) What would be the size ...
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3 votes
1 answer
396 views

Where can I find this formula?

I found this source code written by someone: ...
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6 votes
1 answer
158 views

How to add molecules to a specific location in periodic box using gromacs?

In gromacs using the commands, command_1 gmx insert-molecules -f run03.pdb -ci CL.pdb -o out.pdb -nmol 119 will distribute CL ions in the system randomly, but how ...
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10 votes
1 answer
92 views

Contact Angle (water droplet on a surface)

I have built a CG model of a surface on which I want to place a water droplet (some water molecules), and calculate the contact angle. Has anyone done similar work with gromacs (MD simulation)? First, ...
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2 votes
0 answers
27 views

CHARMM-gui creates empty space between LPS-s and terminates while building e. coli outer membrane with peptides above it

I'm trying to build outer membrane of e. coli with small peptides above it, with CHARMM-GUI. Peptides should be positioned above the membrane, but CHARMM-GUI creates space for them between LPS (...
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1 answer
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Any molecular codes to calculate non-local susceptibility?

I am interested in calculating the non-interacting non-local susceptibility for simple molecules. In principle, if you have a single Slater determinant, then you should just take a sum over the ...
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6 votes
1 answer
111 views

Transforming from CI basis to MO basis

Suppose, one knows the ground state wave function $|\Phi\rangle$ in terms of a slater determinant(SD) basis say, from a Configuration interaction calculation. $$|\Phi\rangle= c_{\text{HF}}\left|\Psi_{\...
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7 votes
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Diffusion coefficient as a function of distance from the position autocorrelation function

I am trying to understand if my idea for the computation of diffusion coefficient as a function of distance is right or not. So, the diffusion coefficient as a function of distance is given by, $$D(z) ...
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8 votes
1 answer
111 views

How to resolve "Error in Cholesky factorisation in cdiag" in SIESTA?

I have worked with the SIESTA code last 2 years. Recently, I faced some errors Error in Cholesky factorisation in cdiag during graphene-BC3 heterostructure ...
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6 votes
1 answer
47 views

Is it possible to simulate the intercalation of hydrogen nanobubbles?

Is it possible to simulate the intercalation of hydrogen nanobubbles into 2D layered materials using first principles calculations such as Density Functional Theory? Would this require a multi-scale ...
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17 votes
4 answers
732 views

What are the physical reasons if the SCF doesn't converge?

I've been mostly using ab initio methods as a routine calculation tool, so even though I know some things from the theoretical side, I still have mostly hands-on experience. One of the things that I ...
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7 votes
0 answers
53 views

Can Markov State Models based on short-term non-equilibrium datasets also capture the dynamics towards equilibrium?

I am non-specialist who is new to the field of computational physics/biology. I have a few questions about the relevance and effectiveness of Markov State Models (MSM) in capturing the dynamics ...
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17 votes
1 answer
1k views

Do we know for sure that all atomic and molecular wavefunctions decay exponentially as r goes to infinity?

Slater type orbitals (STO) are considered to be more accurate than gaussian type orbitals (GTO) for atomic and molecular QM calculations because - among other reasons - they decay with $e^{-\alpha r}$ ...
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8 votes
2 answers
659 views

Is there a benchmark paper that takes into account how often each molecule is studied?

There are many benchmark sets in different branches of computational chemistry and physics, that are frequently used to assess the "average error" of a method for a certain property, on a ...
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6 votes
0 answers
46 views

Any Open-Source, Free Software That Can Be Used to Computationally Calculate Binding Affinity Between Two Molecules?

There are programs out there which calculate the binding affinity between a ligand and a target protein (Autodock 4, Autodock Vina, Chimera... etc). Is there any analogous program that can be used to ...
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10 votes
1 answer
113 views

Recommendation of open source software that could build Heterostructure models visually?

I am looking for open-source software that could help me to build Heterostructure models visually, I've been working with BIOVIA Materials Studio before, but I got no valid license now, so I'd like to ...
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  • 1,601
7 votes
1 answer
81 views

Symmetry group of p-benzoquinone

I am trying to calculate the UV-visible spectrum of p-benzoquinone. In the literature, the point group of p-benzoquinone is $D_{2h}$, but when I optimize this molecule in the ground state with ...
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  • 517
10 votes
3 answers
320 views

How to plot molecules with angles and bond lengths

There are many programs out there where you pass an XYZ coordinate file and the program will give you a visualization of the molecule. I want to make a plot like the one in the picture, with bond ...
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7 votes
2 answers
182 views

How to rotate polarizability tensor depending upon the molecular coordinates?

My question is somewhat related to molecular rotation. I have calculated the polarizability tensor of $\ce{HCHO}$ molecule in PSI4. The output tensor is this, ...
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10 votes
2 answers
307 views

ASE convesion of Trajectory file to XDATCAR

The issue here is while converting a TRAJ file to POSCAR, it works. But, for TRAJ to XDATCAR, it shows TypeError: images should be a sequence of Atoms objects. (...
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8 votes
1 answer
118 views

Confused about the application/definition of improper torsions

The only basic definition of improper torsion/improper dihedral I have is - improper dihedral is formed when we have a central atom bonded to the three atoms. Can anyone help me visualize/help to ...
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8 votes
2 answers
305 views

Building model of Graphene Oxide

I used to build some small molecules using Avogadro. Now, I want to build a large molecule, Graphene oxide which unfortunately doesn't have a definite structure with different levels of oxidation. Can ...
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12 votes
2 answers
406 views

What kind of systems do we need to coarse-grain to observe interesting phenomena?

When I go to talks, I hear the statement "coarse-graining is required to access spatio-temporal scales to observe important dynamical behavior for stimuli-responsive systems" before they go ...
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17 votes
3 answers
2k views

What does ns/day mean in high-performance computing?

In MD simulation benchmarking, you often see performance expressed in terms of ns/day and hours/ns. How do I translate these ...
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  • 1,562
12 votes
2 answers
512 views

Why can MD simulations not handle "exotic" materials?

We are all aware of the fact that MD Simulations using force fields can treat very big systems. But they cannot handle "exotic" materials. Why?
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8 votes
1 answer
414 views

Given the adjacency matrix of a molecule, how can I get a graphical representation using only open source software?

In Huckel Method, by numbering the sp2 carbons in a molecule with conjugated double bonds, we can assemble its secular determinant in a form similar to the adjacency matrix of a graph. Taking trans-...
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8 votes
1 answer
236 views

Calculating compressibility from a molecular dynamics simulation: what is meant by "volume fluctuation"?

I am trying to calculate isothermal compressibility from an NPT molecular dynamics simulation, but am not that experienced and don't know how to use an expression from a paper to do it. The part that ...
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5 votes
4 answers
455 views

How to edit the first line of XYZ file?

...
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3 votes
1 answer
25 views

Question regarding conflicting results of checking the electron-preciseness of isoelectronic species via NBO and EHM calculations

(Cross-posting from Chemistry.SE due to recommendation that this be posted here; see comment section) It is well known that the tert-butyl cation's empty 2p orbital on the central carbon is stabilised ...
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5 votes
0 answers
83 views

How can I add double bonds to Triazine-derivatives for OpenBabel generation of pdbqt files? [closed]

The double bonds are initially present at the sdf file but disappear or are misplaced after .pdbqt conversion. I tried all kinds of combinations using renumbering ...
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2 votes
1 answer
46 views

Determining the geometry of UOx and WOx for (x=1-3)

Is there a way to work out the geometries for the $\ce{UO_x}$ and $\ce{WO_x}$ species for ($x=1-3$). I know that deducing the multiplicity (the number of unpaired electrons) in d and f block ...
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4 votes
1 answer
103 views

Density functional theory and oxygen spin

I would like to perform single-point/geometry-optimization/NEB calculations on systems involving both molecular oxygens and adsorbed oxygens. Reductions by hydrogens are also involved. I am still ...
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6 votes
2 answers
242 views

How to find out the multiplicities of molecules containing d and f block species?

I know that the U atom has four unpaired electrons. Therefore it has a total spin S of 2. This means its multiplicity is 2S+1 = 5. Now consider a complicated molecule such as $UF_6$. In theory all I ...
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6 votes
1 answer
368 views

What is the polarization catastrophe?

I heard about the polarization catastrophe in a talk about polarizable force fields. The speaker talked about how the dipole induction is damped at short range to avoid the “polarization catastrophe&...
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9 votes
1 answer
372 views

I generated Wannier centers but am having trouble understanding how they relate to the atoms in my system: there are more Wannier centers than atoms?

I'm trying to calculate dipole moments from Wannier centers for the first time and there are basics I don't understand and can't figure out from online resources. The software I'm using has a simple &...
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7 votes
0 answers
67 views

Molecular Structure Vectorization for Computational Quantum Mechanics [closed]

What are the different ways that a molecule can be encoded into a vector? My answer to that question would employ machine learning but maybe there are other approaches, perhaps analytical, e.g., graph ...
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8 votes
0 answers
107 views

References related to the molecular distance geometry problem (estimating true distances based on noisy distances)

One aspect of the molecular distance geometry problem (MDGP) described in this PDF, can be written as follows: "Given observations of noisy distances between atoms in a molecule, estimate the ...
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9 votes
2 answers
114 views

Classes of Graphs used in Chemistry

I am looking for common categories of graphs used in chemistry, for math research I am doing in graph theory. When I write categories, the meaning is not for graphs design or types of design, but for ...
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  • 191
7 votes
2 answers
108 views

What quantity to perform CBS extrapolation on for adsorption/binding energies?

When calculating complete basis set extrapolations for quantities, such as adsorption energies or binding energies, which depend on the difference between three quantities (i.e. $E_\textrm{prop} = E_\...
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