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Questions related to Molecular Dynamics Simulation
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14 July 2023 800 1 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 4,771 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 8,948 1 View
Hi everyone, Do you have any idea how we can use NPH ensemble in Gromacs? Do we need to completely delete temperature coupling options and use Parrinello-Rahman as the barostat(or maybe...
10 July 2023 8,650 3 View
gmx_mmpbsa, error,
07 July 2023 8,367 2 View
is thair any one have experience with polymer builder to generate polymers chains from monomers hetero and copolymers I need help please
05 July 2023 5,752 1 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 3,289 3 View
I have the text of a biomedical document and I have extracted the biomedical terms, now I want to create a connected graph that connects all the terms, I am using the Unified Medical Language...
03 July 2023 4,166 4 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 8,693 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 1,212 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 7,124 6 View
I am trying to visualize the change in the molecular geometry along the reaction path using the output from the Polyrate17-C package for a gas phase addition reaction. As mentioned in the Polyrate...
20 June 2023 5,165 0 View
In this strucutre each Bi atom is coordinated with four oxygen and each each oxygen is cordinated with 2 Bi atom. I find it difficult to understand how this layer is named as (Bi2O2). The charge...
18 June 2023 9,049 0 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 3,753 1 View
PDB Code of protein or name
15 June 2023 1,233 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 1,213 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 2,881 4 View
Hi, I am using Malvern's Zetasizer to get the rheological properties of the hydrogel formed with Phytagel containing silica beads entrapped in the said hydrogel. When I am taking the readings...
13 June 2023 2,165 7 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 9,113 13 View
I ran a molecular dynamics simulation which was interrupted at the penultimate stage due to a power cut.
05 June 2023 5,750 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 6,602 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 802 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 960 0 View
I am trying to find out the logic in not identification of hydrogen bond interaction in the charged NH+ from the ligand part with the Asp residue from the protein. That incidence has been observed...
01 June 2023 7,348 0 View