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Questions related to Molecular Dynamics Simulation
I am docking small peptides up to 6 AA chain long. After so many month of trying to find a successful peptide-protein docker, i finally found Swisssdock but now the challenge is how to analyse the...
21 October 2023 2,612 2 View
By classical quantum mechanics we mean original QM of N. Bohr Hydrogen atom before Schrodinger equation and Bohr/Copenhagen superposition interpretation. We assume that classical quantum mechanics...
19 October 2023 8,330 7 View
Hi, I need to generate slate koster files for interaction of Bi2MoO6 with C,O and Cu. Which software can be used for the generation of SK files? Can we use material studio for its generation? how...
19 October 2023 3,015 0 View
Τhe loss of momentum correlations after position estination disturbs the correlations between the complex values, i.e momentum is not deterministically known or via probability density of...
14 October 2023 1,161 2 View
air holes in the crystal fibers
14 October 2023 2,732 2 View
hexagonal lattice and the square lattice
14 October 2023 8,964 1 View
Hi, all I am new to umbrella sampling, I have the done simulation of 2 gold nanoparticles coated with ligand and interaction with 2 different groups: Case 1: with atp Case 2: water But my PMF...
13 October 2023 4,720 0 View
>> dynare DomNX Starting Dynare (version 5.4). Calling Dynare with arguments: none Starting preprocessing of the model file ... Found 22 equation(s). Evaluating expressions...done Computing...
12 October 2023 379 0 View
Do greenhouses gases absorb long wave radiation and trap heat in the atmosphere and greenhouse gas absorb infrared radiation and re radiate it?
08 October 2023 3,975 0 View
While using charmm-gui, there seems to be some error which i have no answer
06 October 2023 9,772 2 View
will LanL2DZ will be Good option..?
05 October 2023 1,060 3 View
Distortions of reality are thought to be driving force in model creation in science Relativity Time is not fundamental, spacetime is Linear ordering of events instead of force altering non-event,...
04 October 2023 9,787 0 View
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29 September 2023 7,728 3 View
I need the CIF file of Na2CO3 having space group C2/m with cell parameters (a=9.0107, b=5.2443, c=6.3053, alpha=90, beta=97.3490 and gamma=90) and cell volume of 295.50. This file is present in...
27 September 2023 8,132 1 View
LAMMPS WARNING: Bond/angle/dihedral extent > half of periodic box length. How to rectify it?
26 September 2023 9,360 1 View
Hello everyone, I am currently facing an issue while attempting to perform MMPBSA calculations. I encounter the following error message: "ModuleNotFoundError: No module named...
22 September 2023 3,216 0 View
can we perform spin orbit coupling calculations for perovskite (non-magnetic). If yes, then what tags can we included in the INCAR file for such a system. please guide me
21 September 2023 3,919 1 View
I am trying to perform simulation of my protein-ligand complex system following Gromacs Protein-Ligand complex tutorial , so during the NVT equilibration using the command " gmx grompp -f nvt.mdp...
15 September 2023 9,421 2 View
Hello, I know that profex, Mercury and MAUD can all fit powder XRD data to structual data given by an CIF file for example. However, I can't find a free software where I can fit only the peaks...
12 September 2023 5,202 7 View
Dear all, I have been trying to create a complex for MD simulation in gromacs of Calcium sensing receptor venus fly trap domain with tryptophan in the binding site as it is part of the crystal...
11 September 2023 9,157 1 View
I did molecular docking using autodock-vina and found great score of binding affinity. But when I dive on to see the protein-ligand interaction I did't found any h-bond among many of my bond...
10 September 2023 5,654 3 View
Does Diindolylmethane interact with or reduce the effectiveness of Androgen Deprivation Therapy drugs bicalutamide and LHRH agonist?
08 September 2023 6,778 0 View
NEWfertilizer is generated using non thermal plasma technology to ionize air and bubble it through water creating dissolved nitrates. The only input is air. Electricity is used to generate the...
06 September 2023 8,168 5 View
Hi I will be working with some constructions to detect relative luciferase activity but I need to know if anyone has worked on this, specifically with the type of detection kit and equipment...
30 August 2023 7,738 0 View