Questions tagged [molecular-modeling]
Questions to do with molecular modeling.
239
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Problematic optimization of excited states
I work with Orca 5.0.4 (without access to version 6.0) on a symmetric metal-centered system. I'm currently running excited state optimizations, and while S1-S3 and T1, T2, and T4 have optimized ...
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How to force which degenerate orbital is occupied during the HF optimization process on Gaussian09?
I am currently running a RHF calculation on a singlet fragment of the central atom in a $D_{2h}$ symmetric linear molecule contained in the $z$-axis (both the $x$- and $y$-axes are degenerate). The ...
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What is the best way to calculate the partial charge?
I'm looking for advice on calculating atomic charges, particularly when dealing with metal atoms in a structure. I'm currently using the RESP method with the following Gaussian input:
...
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How to model drug adsorption on nanomaterial?
I have a substance, a Cu-bisphenanthroline complex, and I want to examine its adsorption on different materials. I am considering carbon and silica, and possibly something else like liposomes to ...
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Are there any software packages to find the minimum number of constraints to fix a molecule structure?
I wanted to know if there are any modules or packages which help in identifying the bonds which should be fixed to make the molecule rigid. For example in $\ce{H2O}$ there are just three (trivial), $\...
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Very high pressure fluctuations in molecular dynamics
I'm performing molecular dynamics simulations through the TIP3F model for water in NpT ensemble. The pressure control is attained by using the bussi barostat, while the temperature one through the ...
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Do oscillator strengths matter when matching theoretical and experimental outcomes?
I use ORCA to do TD-DFT studies. The experimental maximum absorption is esteemed to 445.0nm . Benchmark computations were conducted and this is the exemplatory (part of) the output:
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Should I use ZORA/DKH for my geometry optimization, or only for TD-DFT?
ORCA has implemented a scalar relativistic contracted version of def2-TZVP (with DKH or ZORA), which I used to study a copper-phenantroline system (for geometry optimization and TD-DFT).
My question ...
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How to decouple the Lennard-Jones (LJ) interaction between two particular atoms in a same molecule?
I would like to decouple the lennard-jones (LJ) interaction between two atoms of the same molecule. These atoms obviously doesn't have any bonded interactions between them, so only the non-bonded ...
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Fix the distance restraint between two set of molecules in gromacs
it seems that in GROMACS we can apply distance restraint between two atoms/particles. However, does anyone know if one can apply a distance restraint between whole two set of molecules, like apply a ...
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AMBER fails to generate parameters
I'm new to computational chemistry, and I'm trying to model the enzyme EGFR and a molecule named lapatinib with AMBER. I got a .pdb file of Lapatinib attached to EGFR, and a .sdf file of lapatinib ...
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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 ...
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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 ...
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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, ...
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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?
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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 ...
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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 ...
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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 ...
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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.
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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 ...
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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 ...
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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 ...
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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:
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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 ...
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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?
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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 ...
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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
=...
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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:
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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CCSD calculation between two orbitals
I am trying to calculate the CCSD energies between two orbitals. Suppose I have a system,
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Making Deuterium POTCAR file for optimization in VASP software
How to make Deuterium POTCAR file? i have Hydrogen POTCAR file.
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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, ...
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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
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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 ...
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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:
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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...
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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 &...
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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 ...
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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{\...
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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 ...
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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 ...
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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:
...
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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 ...
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