Questions tagged [molecular-modeling]

Questions to do with molecular modeling.

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5 votes
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Can an atomic structure created after a simulation performed at 251K in LAMMPS be initialized directly to 268K in a separate simulation?

I have a combined mW water and FCC111 Aluminium substrate model to study ice nucleation and adhesion. This simulation is performed at 251K which is the temperature for the actual real-world experiment....
2 votes
0 answers
38 views

how to incorporate size polydispersity in colloidal suspensions

Basically, I'm working on spherical colloids and investigating the phase behavior of these monodisperse colloids using Monte Carlo simulations (Fortran 77 coding). Now I want to introduce size ...
3 votes
1 answer
56 views

Ovito dislocation analysis

How can I append my pipeline in Ovito? I tried to append DislocationAnalysisModifier with Selected atom: ...
7 votes
1 answer
237 views

How is the zero energy defined for molecular orbitals?

In DFT and Hartree-Fock bonding orbitals have negative energies while antibonding orbitals have positive energies. Why is this the case? It seems this is due to the zero-point energy being defined for ...
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5 votes
1 answer
39 views

Generalization of always accepting box upscaling moves in Monte Carlo for a triclinic box

When you are using Monte Carlo scheme to simulate equilibrium phases of convex hard-core molecules, namely, whose energy is infinite when in contact and 0 otherwise in a standard, cubic simulation box,...
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2 votes
0 answers
30 views

Rdkit: How can I get a weighted adjacency matrix where the weights are bond lengths, from the SMILES of my molecule?

Given the SMILES of my molecule, how can I get a weighted adjacency matrix where the weights are the bond lengths, using the Rdkit package and Python?
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5 votes
1 answer
123 views

Binding energy with ONIOM

Do you know how to compute binding energy using Gaussian? I have optimized binding pocket with ligand using ONIOM methodology implemented in Gaussian16. For the high layer B3LYP/6-31+G(d,p) was used, ...
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5 votes
2 answers
140 views

How to do a loop in Ubuntu?

I want to run multiple Gaussian jobs (one after one). I have a folder which contains more than 30 molecules and I want my calculation to start with molecule 1 then when the job is finished, start the ...
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3 votes
1 answer
31 views

Reference-like introductory resources for molecular modelling in drug discovery?

Reference-like introductory resources for molecular modelling in drug discovery? Particularly I want to cover: Underlying chemical phenomena and methods Mathematical methods that have been ...
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4 votes
0 answers
47 views

Molecular dynamics method to simulate a simple fluid

I need to implement the molecular dynamics method to simulate a simple fluid that interacts through the Lennard-Jones potential in a 2D simulation. The idea is to explore how the total energy of the ...
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4 votes
3 answers
380 views

Does the RI method actually accelerate basis convergence of MP2, "by one more zeta"?

It is often said that the resolution of the identity (RI) method accelerates the basis set convergence rate of MP2 "by one more zeta", e.g. that RI-MP2/cc-pVTZ/cc-pVTZ results are close to ...
4 votes
0 answers
36 views

How to make idealized infinite alpha helix or beta sheet?

I'm interested in studying some simple periodic model systems representing proteins. For that I'd like to make pdb files of an alpha helix or beta sheet with idealized coordinates which is infinitely ...
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2 votes
0 answers
21 views

Appropriate choice of force constant of spring to use for Steered molecular dynamics

As per Boltzmann distribution, the variance, or the fluctuation in length squared is given by $$\sigma^2 = \frac{k_BT}{k_{spring}}$$ Since $k_{spring}$ determines how strong the force I am applying to ...
3 votes
0 answers
209 views

Gaussian Software Package: #2070 error (maybe on link0)

I have a computer equipped with two Intel Xeon cpus(6 core @2.67GHz each) and 64GB RAM. I think there is no problem in my gaussian input file except for link0 section. I selected 6 cores and 10GB ram. ...
4 votes
1 answer
27 views

List of properties of molecules categorized by the number of atoms?

Is there an online database having information on molecules with a certain number of atoms? For example, properties of tri-atomic molecules? There is this table that I got from NIST which gives a few, ...
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7 votes
2 answers
424 views

Do bonds between the atoms influence ab-initio energies?

As you know, oxygen has two available states. However, the picture above illustrates oxygen (red) has a just one bonding with one carbon. I am kind of afraid it makes differences compared that an ...
7 votes
1 answer
101 views

Water Dimer and Free Energy Perturbation (FEP)

I am trying to understand the FEP in the context of water dimer. Let's say I want to calculate $\Delta A$, the free energy change for the following reaction: $\ce{H_2O +H_2O\rightarrow H_2O-H_2O}$, ...
1 vote
0 answers
30 views

Gaussian(Software): What does atomic orbital contribution mean?

Example Molecule: C60 (Fullerene) Route Section: #p B3LYP/6-311G(d) guess = read geom = check pop = full Question: What information can I get from atomic orbital contributions? I've calculated atomic ...
3 votes
1 answer
59 views

Determining orbital occupation through MO shape (Biorthogonalized molecular orbital)

Can it be determined whether a biorthogonalized molecular orbitals is singly occupied just from its shape? You can see the picture below, describing biorthogonalized molecular orbitals' shapes of $\ce{...
6 votes
2 answers
91 views

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 ...
3 votes
0 answers
75 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
50 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
668 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
0 answers
39 views

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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4 votes
1 answer
124 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
0 answers
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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
59 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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8 votes
1 answer
376 views

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 ...
4 votes
0 answers
71 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
2k views

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 ...
2 votes
1 answer
64 views

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
398 views

Where can I find this formula?

I found this source code written by someone: ...
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6 votes
1 answer
459 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 ...
10 votes
1 answer
172 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, ...
2 votes
0 answers
35 views

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

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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7 votes
1 answer
51 views

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
117 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_{\...
user avatar
7 votes
0 answers
101 views

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) ...
8 votes
1 answer
208 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 ...
6 votes
1 answer
48 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 ...
17 votes
4 answers
903 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 ...
user avatar
7 votes
0 answers
66 views

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

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
674 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
52 views

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

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
215 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 ...
  • 1,883
7 votes
1 answer
101 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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10 votes
3 answers
489 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 ...
7 votes
2 answers
220 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, ...
10 votes
2 answers
554 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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