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Questions related to Molecular Dynamics
I found that hydrophobic comprised of many types such as pi-sigma interaction, alkyl interaction etc. What are the differences between them? Can someone enlighten me? I am still new in this field....
27 September 2022 5,634 1 View
additionally, how can we calculate different cooling rates when we melt a system up to 3300k and quench at room temperature for 10000000 steps
06 September 2022 1,387 7 View
I am looking for ideas to quickly and cost-effectively confirm in the lab how well different types of plastic-wax mixes disolve in bitumen in order to have an idea of how my molecular models are...
10 August 2022 2,118 0 View
Any specific reason for the unfavorable Bump. What is an Unfavorable Bump?
24 July 2022 1,109 0 View
Residues in α-helices typically adopt backbone (φ，ψ).How can I get the number of residues localized within (φ，ψ) in a gromacs simulation?
09 July 2022 1,424 0 View
Colleagues, I need suggestions for PDB complexes with ligands (organic molecules) that prove difficult to validate by redocking, regardless of the program. Suggestions in the comments, and thanks...
04 June 2022 4,184 0 View
I am using PyRx as platform when I load macromolecule and ligand, the molecules get loaded. When I Dock I get this message " >>Python 2.6.5 (r265:79096, Mar 19 2010, 21:48:26)" Can anyone...
03 May 2022 5,747 4 View
I have some apoptotic proteins identified from breast cancer datasets. I have a general queres in my mind. 1) How does apoptotic proteins function in cancer cells? 2) Would inhibiting an...
22 March 2022 214 4 View
Hello, I have ran MD simulation using NAMD and CHARMM36 forcefield and want to calculate RMSD values of multiple residues.(EX: RESID1 to52,133-193,281 to 296)How can I calculate this using VMD? I...
18 March 2022 5,683 4 View
Dear researchers Would you please guide me about the temperature of quantum espresso calculations? For example, relax analysis or phonon analysis is in 0 Kelvin or room temperature? Thanks
05 March 2022 117 4 View
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 9,493 4 View
Body centered cubic
04 February 2022 9,822 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 8,131 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 791 2 View
Please give your explanation
01 January 2022 1,441 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 9,782 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 8,970 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 5,515 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 2,383 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 7,840 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 987 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 2,397 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 3,965 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 887 0 View