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Questions related from Bahareh Bamdad
Dear all, I need to perform an MD simulation of a Pt cluster on a carbon surface using the LAMMPS software. I have used the EAM potential to describe the Pt-Pt interaction. The simulation...
06 February 2025 8,433 5 View
Dear All, I have a PDB structure for a complex and large polymer. I need to perform MD simulations using the OPLS-AA force field. I obtained the force field parameters from LigParGen and created...
12 July 2024 5,329 0 View
Dear all, I need to calculate the UV-Vis spectra with an explicit solvent. For that, I think I need to conduct some MD simulations, extract the structure from the MD results, and then perform...
16 April 2024 4,883 0 View
Dear all, I'd like to run some molecular dynamics simulations on a system that includes a metal organic framework (MOF) and a protein. Can I get reliable results if I keep the MOF rigid during...
18 May 2023 8,798 0 View
Dear all, I need to run molecular simulations on the NU-1000 MOF. Its proton topology is [Zr6(3-O)8O8H16]8+ in a staggered pattern, according to the paper. I'd like to know how I can add hydrogen...
01 May 2023 8,266 0 View
Hi all, I need to do a molecular simulation for 1EVQ protein which contains TRS. Some Literature reviews show that TRS could be a buffer. On the other hand, I know that in preparation of a...
22 December 2022 3,404 2 View
Dear people, I am confused about LUMO orbitals in photovoltaic solar cells. According to the literature, Voc (open circuit voltage) is related to the HOMO orbital of donor and LUMO orbital of...
17 August 2020 1,726 4 View
Dear people, I have optimized a dimer (each monomer contains about 50 to 60 atoms) structure in its equilibrium distances (I have done a rigid scan to find the equilibrium distance between...
06 August 2020 7,869 1 View
Dear people, I am a newbie in EEG signal processing and classification. I have recorded EEG signal for some subjects. By far, I have done pre-processing and artifact elimination, feature...
30 June 2020 678 2 View
Dear all, I need to calculate the amount of Jsc for solar cell using quantum mechanics approach. As the Jsc is the integration of the Air mass spectrum, is it possible to calculate it according...
01 December 2019 5,619 2 View
Dear all, I need to calculate binding energy calculation between a protein and a mof using gmx_MMPBSA. I have used Gromacs software to perform the following MD simulation steps: 1. I manually...
01 January 1970 4,534 2 View
Dear all, I need to perform MD simulations for a system comprising a protein and a polymer using the GROMACS software. I have two questions regarding this: In reality, the polymer is a part of...
01 January 1970 10,021 4 View
