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Questions tagged [molecular-modeling]

Questions to do with molecular modeling.

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What software is fit for calculating an atomic and electronic structure of a newly formed nanocluster after injecting impurities into an initial one?

Let's suppose there is a nanocluster and its structrure is known. The problem is to inject impurities into this nanocluster. The impurities can be injected in different quantitites but consist only of ...
SFriendly's user avatar
  • 967
3 votes
0 answers
30 views

How to resolve discrepancy between simulated and analytical diffusive particle statistical behaviour in one-dimension?

Assume a scenario where a Brownian particle with diffusion coefficient $D$ is emitted in a 1-D environment from $z=d$, the reflecting wall is at $z=0$, we know analytically that the PDF of such a ...
Userhanu's user avatar
  • 131
4 votes
1 answer
54 views

Relation between force constant of the bonded parameters, time constant and the dynamics of the system

I want to understand these things in both intuitive and non-intuitive ways. In some cases, we constrain hydrogens so that we can run molecular dynamics at a higher time step than we normally would, ...
Roshan Shrestha's user avatar
5 votes
1 answer
47 views

Forcefield parameterization techniques

Suppose I have a novel synthetic protein. I want to find the classical forcefields that accurately models the dynamics and thermodynamics of the protein. How do I do that?
Robin's user avatar
  • 61
6 votes
1 answer
116 views

Explain ab initio molecular dynamics like I'm five

In Kashiwaya, S., Shi, Y., Lu, J. et al. Synthesis of goldene comprising single-atom layer gold. Nat. Synth (2024) monolayers of hexagonal Au(111) planes are produced and released into solution where ...
uhoh's user avatar
  • 2,034
1 vote
0 answers
61 views

Code to build the monoclinic crystal lattice

Benzoic acid exists as a solid at room temperature. So, I want to build a monoclinic crystal structure of this molecule. Is there any code available to do that? Thanks. Edit: Is there any way to build ...
Roshan Shrestha's user avatar
4 votes
0 answers
21 views

How to relate the degree of oxidation with the C/O ratio for the nanomaterials like graphene oxide?

I am currently working on the molecular modelling of Graphene oxide. It has different oxygen containing surface functionalities, so different degrees of oxidation. I am wondering if there is anyway to ...
NM_curious's user avatar
8 votes
3 answers
217 views

Different results from MP2 calculations on same geometry in ORCA

I am trying to do a segmented potential energy scan around a dihedral for a molecule. I have optimized the geometry to a minima, and the scan runs from [-180, 180] in steps of two points at a time. ...
Hemanth Haridas's user avatar
3 votes
0 answers
12 views

Diblock building in Biovia material studio

I am trying to build polystyrene and polyethylenepropylene diblock chains. When I assign head and tail and build diblock chain I could see that the atom numbers get flipped, meaning that head and tail ...
Princy David's user avatar
5 votes
0 answers
32 views

How can calculate length or coordinate of any molecule in different quantum state [like (rotational quantum state)j=2] with any software or code?

How can one determine the bond length of a diatomic or tri-atomic molecule(rot. state J=3 and vib. state v=2) from its ground state bond length (x angstrom) using computational tools or programming ...
Rubi Agrawal's user avatar
8 votes
5 answers
761 views

How to identify small molecules in a structure without bonds

If I have an XYZ file with a cluster of a dozen of molecules: water, $\ce{O2}$, $\ce{H2}$, $\ce{H2O2}$. A human may easily identify these molecules. But how to do it automatically? I need to identify ...
user36313's user avatar
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4 votes
0 answers
41 views

How can we identify the symmetry of the molecule from its IC table?

We are given the IC table for benzene in CHARMM format, which can be written as follows: ...
Hemanth Haridas's user avatar
7 votes
2 answers
370 views

Restrain a protein to be helical in an MD simulation

I have a very small part of a protein that is supposed to be helical. However, in molecular dynamics simulation, it unfolds and gets into extended conformation. Is there any way I can force it to stay ...
Roshan Shrestha's user avatar
2 votes
1 answer
35 views

How to parse GDB SMI file?

Reymond Research Group from Bern University has created [GDB-17][1], a compendium of molecules in SMILES format. The file is in smi format, how do I parse the molecular structure in xyz from this?
ananta's user avatar
  • 221
5 votes
1 answer
109 views

How are z-matrices represented in the various matter modeling packages?

Is there a standardized format that is commonly used across molecular simulation (or QM) software packages to store z-matrix information about a molecule? For instance, in CHARMM, which is a Molecular ...
Hemanth Haridas's user avatar
2 votes
0 answers
28 views

Creating 1M NaCl solution using PACKMOL

I want to create a 1M NaCl solution in a 1nm X 1nm X 1nm size cell using PACKMOL. So, what should be the NaCl:H2O ratio for this concentration? My calculation is - 1M NaCl = 1 mole NaCl + 1000 mL H2O =...
Abdullah Shahriar's user avatar
7 votes
1 answer
76 views

OpenMOLCAS error while running CCT in &CCSDT module

I am trying to perform a coupled cluster calculation at the CCSD(T) level using OpenMOLCAS. My input file is the following, in which I am using default values for most of the key inputs: ...
Jaafar Mehrez's user avatar
4 votes
0 answers
32 views

Query regarding individual polarization calculation using CP2K

I am seeking assistance in calculating the individual polarization matrix from CP2K. While utilizing the Polar input under FORCE_EVAL -> PROPERTIES -> LINRES -> POLAR, I observed that the ...
Simantini Paul's user avatar
5 votes
1 answer
78 views

How can one create various arrangements of two or more types of atoms (like O, N etc.) with distinct coverages on a metal surface?

How can I modify the procedure described in this answer to achieve adsorption of two or more types of atoms on a surface, each with distinct coverages? Is there an extension to the described method ...
Rubi Agrawal's user avatar
3 votes
1 answer
98 views

Orthonormality of AOs and MOs in PySCF

I have a basic question about how to calculate molecular-orbitals from atomic-orbitals in PySCF using the self-consistent field approach. My understanding mathematically is as follows: we start with a ...
Solarflare0's user avatar
7 votes
1 answer
362 views

Why use PySCF/OpenMolcas instead of VASP/QuantumESPRESSO

While I am aware that VASP and QE are widely used for solid-state materials and PySCF/OpenMolcas are primarily designed for molecular systems. I want to know why should I use PySCF/OpenMolcas for ...
Jaafar Mehrez's user avatar
4 votes
0 answers
72 views

Solvation_analysis subpackage for MDAnalysis multi-atom solute

I have a simulation trajectory from DFTB+ for 1 NaNO3 in 32 H2O molecules. The trajectory is in xyz format and I converted a frame of xyz to pdb using openbabel to serve as topology input. I am ...
bhopshang's user avatar
  • 233
6 votes
1 answer
94 views

Creating a Hypothetical Hexagonal Monolayer Structure Similar to MoS2

I am seeking guidance on how to generate a POSCAR file for a hypothetical monolayer with a hexagonal structure similar to MoS2. Can anyone provide me with a step-by-step procedure or recommend any ...
Farah Shehzadi's user avatar
6 votes
1 answer
153 views

MOPAC: Is there a simple way to display geometry trajectories

I would like to display MOPAC geometry trajectories for structure minimization and transition state searching. Is there a simple way to achieve that ? Avogadro can display only final geometry from ...
Miro Iliaš's user avatar
4 votes
1 answer
401 views

Blind docking and targeted docking

I used Autodock Vina and UCSF Chimera to perform blind and targeted docking on a protein from the RCSB database and a molecule I had optimized with Gaussian software.The results are as follows: The ...
sarra6's user avatar
  • 579
4 votes
0 answers
61 views

CCSD calculation between two orbitals

I am trying to calculate the CCSD energies between two orbitals. Suppose I have a system, ...
Pro's user avatar
  • 1,024
3 votes
1 answer
107 views

Making Deuterium POTCAR file for optimization in VASP software

How to make Deuterium POTCAR file? i have Hydrogen POTCAR file.
Rubi Agrawal's user avatar
3 votes
1 answer
109 views

Cannot reproduce excitation energies in Orca

I do TD-DFT studies in Orca 5.0.3 on porphyrin system and hence at the very beginning I need to pick functional that reproduce excitation energies. The experimental reported values equal: 691, 656, ...
farmaceut's user avatar
1 vote
1 answer
78 views

What is the best way to optimize molecules with 8000 atoms. This includes C,H,O,N,Si

My molecule includes C,H,O,N,Si
AKM's user avatar
  • 11
2 votes
1 answer
21 views

Geometry of H2O in the v=1 vibrational state for AIMD simulation

This is a follow-up to my recent question: Algorithm for finding the v=1 state of an H2O molecule I want the geometry (atomic positions) of the H2O molecule in the v=1 state. How are initial ...
Nidhi Tiwari's user avatar
2 votes
0 answers
62 views

Error with running GROMACS with SLURM [closed]

I am running into errors while submitting a job for a basic MD Simulation with HPC on SLURM. My sbatch script reads as follows: ...
Pranoy Ray's user avatar
  • 1,637
1 vote
1 answer
28 views

Algorithm for finding the v=1 state of an H2O molecule

In the context of simulating the dissociation dynamics of an H₂O molecule on a metal surface, what algorithm is employed for generating the initial state of a tri-atomic non-linear molecule, such as H₂...
Nidhi Tiwari's user avatar
5 votes
0 answers
75 views

What do Negative Atomic Orbital Contributions in a Mulliken Population Analysis mean?

I am performing a Mulliken population analysis (MPA) for a molecular system of interest (calculated with B3LYP/Def2-TZVP). I am analyzing the LCAO-MO coefficients/contributions associated with each &...
Kevin Freddo's user avatar
4 votes
1 answer
114 views

How to orthonormalize a set of Molecular orbitals?

I am using PySCF, and checked that the molecular orbitals(MO) from the HF calculation are orthonormal. If S is the Overlap matrix, and V is the matrix of the MO coefficients, It can be seen from the ...
Pro's user avatar
  • 1,024
6 votes
2 answers
399 views

How may I solve the radial Schrödinger equation?

I want to solve the radial Schrodinger equation for a Carbon atom with all six electrons. The equation I want to solve is for $r>0$: $$[\frac{-\hbar^2}{2m}\frac{\partial^2}{\partial r^2}+ \frac{\...
L Maxime's user avatar
2 votes
1 answer
270 views

Choice of SMASS for AIMD simulations in VASP

How can one verify that the values (0, 1, 2, and 3) in the SMASS parameter correspond appropriately to the NVT ensemble(Nose-Hoover thermostat) in the context of an ab initio molecular dynamics ...
Rubi Agrawal's user avatar
7 votes
2 answers
171 views

Why is electron correlation called the "chemical glue"?

A significant part of quantum chemistry involves developing methods that go beyond the Hartree-Fock theory which treats electron-electron interactions through a mean-field approach. From what I ...
Fracton's user avatar
  • 271
3 votes
1 answer
144 views

having trouble to get the NPT working

I am currently encountering challenges in successfully conducting NPT simulations in LAMMPS for a triclinic cell persistently remain unchanged throughout the NPT simulation.my input file is: ...
Ati's user avatar
  • 31
4 votes
1 answer
65 views

Povray rendering of Jmol visualization appears brighter

I would like to use Povray to render nice-looking graphics of molecules, which can be exported from visualization softwares like Jmol. However, I have noticed that the color of the rendered graphics ...
Jingyang Wang's user avatar
7 votes
1 answer
78 views

Numerical atomic orbitals vs Gaussian-type orbitals for molecular calculations

Gaussian-type-orbitals (GTOs) are the work horse of modern molecular quantum chemistry calculations. They are computationally efficient and allow for analytic evaluation of integrals. However, there's ...
Fracton's user avatar
  • 271
2 votes
1 answer
50 views

How to make initial trajectory for incident A2 molecule on any surface?

I want to write code to simulate the impingement of any molecule on a surface at different (r, theta, and phi) angles in XYZ format.
Rubi Agrawal's user avatar
6 votes
1 answer
184 views

How to convert MoO3 bulk structure to MoO3 (010) plane surface via VESTA software?

Convert MoO3 bulk structure to MoO3 (010) plane surface via VESTA
Rubi Agrawal's user avatar
6 votes
1 answer
94 views

Is it essential to include solvent cage effect in radical reactions?

My question is straightforward and is outlined in the post title: Is it essential to include the solvent cage effect in radical reactions during the computational estimation of Gibbs free energies and ...
farmaceut's user avatar
5 votes
1 answer
55 views

Generating a pseudopotential for graphene: Is it done on an individual carbon atom, or on an entire unit cell of graphene?

Let's take the example of a 2D graphene layer. The objective is to do an electronic calculation with only the valence electrons with a plane wave basis. Hence the need to pseudize the core electrons ...
mle's user avatar
  • 1,031
4 votes
2 answers
160 views

Post-hartree fock calculation with localized Molecular orbitals in PySCF

I have localized the canonical Hartree-Fock orbitals for a molecule in PySCF. Now I want to perform ccsd calculations with these localized orbitals. Is it possible with pyscf? Example with CCSD with ...
Pro's user avatar
  • 1,024
6 votes
0 answers
67 views

Updated book/chapter or review article with broad perspective on computational chemistry

I really like Frank Jensen's "Introduction to Computational Chemistry" because it provides a broad perspective, starting from first principles and extending to surveys of current methods for ...
sunfishstanford's user avatar
3 votes
0 answers
76 views

Using GPyTorch for GPR together with the SOAP-Kernel

My goal is to use a Gaussian Process Regression (GPR) model with the GPyTorch library with the SOAP (smooth overlap of atomic positions) descriptor that can be obtained with the DScribe library. I ...
C_Swann22's user avatar
  • 543
3 votes
0 answers
48 views

Running molecular docking simulation between two proteins

i did run docking simulation between two proteins on HADDOCK server but now i want to run a simulation of complex (protein+ligand and protein) is it possible with HADDOCK and how can i use it best ...
Imane Yamari's user avatar
3 votes
0 answers
173 views

Advise in generating ESP surfaces from Gaussian .cube files using the IQmol software

I am trying to generate an ESP surface of a Gaussian09 calculation using the iqmol software. I have used Gaussview to visualize the ESP surface by generating .cube files from .fchk files (using the ...
Kevin Freddo's user avatar
6 votes
1 answer
157 views

How are 2-electron integrals usually computed?

I want to compute 2-electron coulomb integrals. When the Primitive Gaussian is not centered at 0, my quadrature scheme fails unless I increase the number of quadrature points. I am currently using a ...
mle's user avatar
  • 1,031

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