Contact experts in Molecular Dynamics Simulation to get answers
2,213 views 3,179 posts
Questions related to Molecular Dynamics Simulation
I have done a mechanistic study (I am a beginner and passionate about computational chemistry) to find the reaction pathway in Jaguar Schrodinger. It is a bulky palladium complex and reactants...
24 April 2023 8,451 5 View
I am facing this error in gromacs, can anyone help me to solve this error.
21 April 2023 3,403 3 View
i want to draw a structure of Mn/NiCo-LDH in Material Studio any body can help me please?
19 April 2023 3,309 1 View
Hi, as my question already indicates I would like to do some multivariate analysis of my proteomics data as I have multiple characteristics in my samples. I have successfully used MetaboAnalyst...
19 April 2023 1,829 3 View
I am conducting a molecular docking study using peptides as ligands. I successfully ran the docking process using autodock vina, and when I viewed it using Discovery Studio, I realized that the...
18 April 2023 8,668 7 View
I am currently trying to develop an assay to test the binding affinity (Kd) of a binding inhibitor to its target, through the displacement of a fluorescent ligand that is pre-bound to the target....
18 April 2023 7,676 1 View
The gold nanoparticle was synthesised through Turkevich method. And also kindly suggest ways to work towards lowering the PDI index.
16 April 2023 8,610 1 View
As I am new to the castep I don't know which parameter should be selected for CuO nanoparticle. I want to use LDA+U potentials. I Want the calculations
16 April 2023 2,375 4 View
Ph.D student Dhaka university of Engineering and Technology(DUET) [email protected]
14 April 2023 3,798 4 View
I am using TS BERNY to optimize the transition state guess structure for my sn2 reaction mechanism. However, when I proceeded to do qst3 calculation, I would receive an error link 9999 all the...
14 April 2023 5,771 3 View
This is a hydroxyapatite sample-2 that was calcinated at 900 degrees Celsius, can you help me describe its morphology based on your experience? I think my sample is very much aggregated in my...
13 April 2023 8,689 3 View
Greetings. Up until now didn't need to quantify minerals, a qualitative analysis was enough, but I wonder if needed what are the best and more feasible/acessible methods to quantify the...
12 April 2023 4,066 3 View
Hi, dear friends online. I am a fresh person in bioinformatics with little understanding. but I need to learn to analyze RNA-sequencing data. I think python is simple, I want to use it to...
06 April 2023 2,607 3 View
I'm using LUVs as membrane models to study drug-membrane interaction. My composition of liposome is POPC : CHOL. I was confused about the selection of a buffer system for my liposomes. So far, I...
06 April 2023 6,783 3 View
I performed a single point energy calculation using ONIOM in Gaussian 09. In my ONIOM calculation, I included 18 residues and the ligand in the high layer, while the rest of the enzyme was in the...
06 April 2023 2,582 3 View
I have already used hydrogen bond plug-in but the graph is showing no hydrogen bonds in all frames.
05 April 2023 8,930 3 View
I'm trying to optimize a large number of structures( above thousand) with 60 atoms in each. I need a cheap method for optimization. I came across DFTB , which can be helpful for my calculation....
02 April 2023 124 3 View
Are their any advantages of using mixture of two solvents rather than one solvent for exfoliation of 2D nanomaterials?
31 March 2023 2,062 2 View
I am facing this error while nvt simulation constantly i am done trying adding -dflexible flag using steep integrator during em also and nvt,mdp also,still error persists how to resolve it , i am...
29 March 2023 3,579 0 View
I am working on membrane lipids and am entirely new to the field. Currently, I am focusing on heart cell membranes. I need the exact composition of lipids present in the human myocardial membrane....
25 March 2023 4,041 2 View
I am currently using VASP, where I want the system to be charged. I add or remove electrons but due to the VASP artifact it adds the background charge to the system. I am looking for a way, where...
22 March 2023 4,335 1 View
A pH of 5.5 would mean 3.16*10^-6 mol/L of H+ concentration. When I convert it into number of molecules per cubic Angstrom, it would be 1.9*10^-9 molecules. It means the box length (assuming...
20 March 2023 560 4 View
Hello to all, I need to perform a standard curve for metagenomic analysis with qPCR, of Treponema Denticola and Pseudoramibacter Alactolyticous, using the 16S RNA copies of my DNA. As well I...
18 March 2023 812 3 View
I ran gromacs with command: grompp -f ions.mdp -c protein a_solv.gro -p topol.top -o ions.tpr. and yielded a Fatal error: number of coordinates in coordinate file (solv.gro, 57741)...
16 March 2023 7,047 1 View