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Questions related to Molecular Dynamics
I want o read the UPF files from Quantum Espresso in python to extract the projectors and partial waves. Is there a package for this already? Also, where can I find a documentation describing the...
12 February 2022 9,553 4 View
Body centered cubic
04 February 2022 9,903 0 View
Sometime this may be a silly question because I'm new to this field. In 3Drefine server, it mentioned that it applies atomic-level energy minimization on the optimized model using a composite...
01 February 2022 8,189 4 View
Hello, I want to grow Mycobacterium smegmatis bacteria on Lb agar and lb broth medium. Do you have a protocol on how to enlarge? Could you help?
11 January 2022 854 2 View
Please give your explanation
01 January 2022 1,526 0 View
That is to say the Miller indices of the crystal phase of Sr (PO3) 2 with their interreticular distances dhkl and the angles of diffraction? And what is the formula for calculating the cell unit...
30 October 2021 9,862 6 View
How is the value for the spring constant (force/time units) and velocity (distance/time units) determined for any Steered Molecular Dynamics simulation? Is there an exact science behind it or is...
20 September 2021 9,052 1 View
Hi, I built two polymer chains of PET (with the build homopolymer) in the material studio software, now I want to develop it's amorphous cell. But the error " Unable to analyse internal graph: the...
17 September 2021 5,583 2 View
Hello, everyone! I've been working on this spin-orbit coupling thing.Spin-orbit coupling can induce spin-polarization in non-magnetic materials, which gives rise to what is called as spin texture...
11 September 2021 2,454 2 View
is it possible to do Molecular dynamics (MD) calculations using Gaussian software (Gaussian 16). does anyone know any good instructional resources?
08 September 2021 7,934 3 View
How to calculate mean square angular displacement ? Do we need any periodic boundary conditions if at each step angle is updated using theta(t+dt) = theta(t) + eta(t) , where eta(t) is a gaussian...
07 September 2021 1,071 8 View
That is to say a method or software for calculating the Buckingham potential parameters between two atoms such as Sr-Sr, Sr - Eu .... to use in the simulation of a matrix of glasses by molecular...
03 September 2021 2,468 4 View
I have successfully made a bilayer with just a receptor for simulation in GROMACS and it works. However, when I try to make a bilayer with receptor-ligand complex in CHARMM-GUI, it fails. How can...
17 August 2021 4,040 0 View
I am trying to simulate an ice adhesion test in LAMMPS using fix SMD. By assigning a pre-determined spring stiffness and control velocity, I am able to achieve delamination of the ice from the...
16 August 2021 975 0 View
I have a coarse-grain molecular dynamic performed in Gromacs. I am interested, in computing the distance between an atom (bead) and a group of atoms (beads), that we can see as a plane. Thanks...
12 August 2021 6,159 4 View
Is GAN a best model for video and audio anomaly detection? If any other algorithm best suited for predicting audio and visual anomaly BOTH. Please do share with me. Regards,
12 August 2021 9,753 0 View
Hi I am kind of new of 16SrRNA data analysis. I just was wondering if I have metadata with many variables , some of them would be expected to have a stronger influence than others on...
11 August 2021 7,423 4 View
Hello, can you help me interpret these results? It is a 100 ns molecular dynamic of a receptor-ligand complex, red is the ligand. Is there a guide or paper to interpret these results? I really...
10 August 2021 9,018 3 View
I want to parameterize a few molecules. I need of course torsional, dihedral angles, charges , etc. What is the most popular program for that right now? I know that gaussian is quite popular, but...
02 August 2021 224 2 View
Dear all, I have the intention to perform molecular dynamics (MD) simulation of carbon nanotubes (CNT) using Drude polarizable force field implemented in NAMD. Initially, I used CHARMM-GUI to...
25 July 2021 2,115 1 View
Hi MD community: I encountered some problems while generating psf file. As we know, PDB only assumes atom names containing up to 4 characters. However, if the atom name in CHARMM topology is more...
24 July 2021 5,492 1 View
I have generated a complex of antigen and antibody using haddock and used that cluster for MD run using Gromacs. Now I need to find out the inter hydrogen bonds formed between antigen and antibody...
22 July 2021 5,429 3 View
I´m looking for the best configuration to build a workstation to run molecular dynamics simulations of proteins in microseconds. It´s even better with the GPU is compatible with CUDA 11 (NVIDIA).
22 July 2021 5,669 5 View
Hii, I want to know if it is a good choice to do model refinement with online server like 3D refine after model generation instead of Molecular dynamics? I have run the molecule simulations up to...
20 July 2021 1,089 8 View