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Questions related to Molecular Dynamics Simulation
I have seen in many studies, oxygen is used as the plasma gas source to produce ozone in the plasma chamber. But my first question is, are there any advantages if ozone is directly used as the...
04 August 2023 8,990 2 View
I conducted a 100ns simulation of my docked complex, obtaining a maximum RMSD of 4.2 Angstroms and an average of 3.1 Angstroms. Can someone help me how can I justify this high RMSD? I have...
31 July 2023 4,245 13 View
I had made a simulation box, and then after made two plates. During equilibration the atoms moves around the 'Z' axis of the simulation box. As in zhi i had taken 10. region allbox block -30 30 0...
24 July 2023 789 3 View
Please get in touch if you are willing to cooperate on a research paper with some computations on Thero-Calc. You must have a license to use the Thero-Calc software. My...
21 July 2023 1,820 3 View
First did the NVT equilibration using below mdp file: title = OPLS Lysozyme NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog...
14 July 2023 6,682 0 View
Hello all. My question goes back to the use of representative volume elements for modeling structures and boundary conditions needed to solve RVE in a finite element model. Assume that there is a...
13 July 2023 4,740 5 View
This question deserves to be posed and clarified. It is at this price that we will be able to consider an improvement involving analyses including new concepts. The answer to this question is...
12 July 2023 8,899 1 View
gmx_mmpbsa, error,
07 July 2023 8,333 2 View
I have been using PRODRG for small molecules topology for years, but now I can't access it, I have emailed its developers but couldn't get any response. I want to use Gromacs forcefield, so I have...
03 July 2023 3,249 3 View
Hi, I am looking to conduct rheometric experiments on water or hydrogels whose viscosity is very less. Should I use Dynamic light scattering or a rheometer?
27 June 2023 8,655 14 View
Hello all, I want to run a Molecular dynamics simulation by using Gromacs and OPLS AA force field. I'm getting the above error when I tried to run the energy minimization step. Now I don't...
21 June 2023 1,172 3 View
I have been reading the following article on peptide structure prediction. https://www.biorxiv.org/content/10.1101/2022.02.17.480937v1.abstract I wanted to know whether alpha fold 2 can be used to...
20 June 2023 7,067 6 View
Hi all, I am trying to coordinate zinc to the NMR structure PDB ID: 1sp1 (a C2H2 zinc-finger) using HADDOCK. To make it clear, the PDB structure is zinc coordinated, and I am using it as a system...
15 June 2023 3,702 1 View
PDB Code of protein or name
15 June 2023 1,197 4 View
I performed protein ligand complex simulation in gromacs. To obtain PCA and FEL graph, used gmx covar, gmx anaeig and gmx sham module of gromacs. For further analysis, I am in need of lowest...
13 June 2023 1,183 0 View
I am a M.Sc. student. I have successfully expressed my protein in soluble part using a solubilizing tag. I faced problems in Ni-NTA purification, as protein was not binding to the column. So, I...
13 June 2023 2,850 4 View
What is the mechanism behind this behavior? Is it due to the longer molecular chain of UHMWPE, which prevents the formation of a crystalline layer?
06 June 2023 9,080 13 View
I ran a molecular dynamics simulation which was interrupted at the penultimate stage due to a power cut.
05 June 2023 5,721 2 View
Hi Collegues, To calculate entropy (T*S) and Gibbs (G) free energy of electroreductions using computational hydrogen electrode (CHE) model (according to this equation, G = E + ZPE - TS + U), can...
05 June 2023 6,551 0 View
I have a protein which has five different components, and these were isolated separately. So is it possible to club these individual fragments together using any tool/software? And if there is/are...
01 June 2023 763 5 View
1. What is the correct pentapeptide sequence of ELPs: GVGVP or VPGVG? 2. Does the sequence "GVGVP" also encode the ELP protein? 3. What differences can be seen if we change the ELP pentapeptide...
01 June 2023 921 0 View
I have the free energy landscape data how do i get this??
28 May 2023 5,118 1 View
my work on molecular docking, pharmacokinetics, DFT KINDLY SUGGEST
27 May 2023 3,029 1 View
I need to use the AutoDock program, but I tried both versions 1.5.6 and 1.5.7. I had no problem loading, my only problem is that when I open the program, the loading remains around 9% in the...
23 May 2023 6,104 3 View