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Questions related to Molecular Dynamics Simulation
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 2,439 4 View
Ph.D student Dhaka university of Engineering and Technology(DUET) [email protected]
14 April 2023 3,857 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 5,842 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 8,779 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 4,125 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 2,679 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 6,851 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 2,640 3 View
I have already used hydrogen bond plug-in but the graph is showing no hydrogen bonds in all frames.
05 April 2023 8,998 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 202 3 View
Are their any advantages of using mixture of two solvents rather than one solvent for exfoliation of 2D nanomaterials?
31 March 2023 2,117 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 3,660 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 4,116 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 4,415 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 615 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 877 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 7,103 1 View
I have successfully installed MGL tools 1.5.7 in windows 11. After the installation is finished, when I run "AutoDockTools" by double clicking the icons on the desktop, the windows command prompt...
16 March 2023 9,258 4 View
Hi every body. I want to do a MD in gromacs for protein but it have a non standard residue. Somone who tell me how I can to do it? Which programs I should to usage? or some tutorial that I can to...
15 March 2023 4,268 4 View
I am working on MD simulation of a nanocomposite .Based on some reactions ,I need to use reaxff forcefield for a better insight. But a force field file for B,N,Si,C,O elements is not available.I...
14 March 2023 4,195 3 View
How does a positive value indicate better binding energy for MM-PBSA binding free energy calculations?
12 March 2023 8,407 5 View
Hello I want to melt the polymer, but the viscosity of the polymer in the molten state is high. Is there a way to reduce the viscosity of the polymer melt (not the viscosity of the polymer solution)?
11 March 2023 5,362 5 View
Can anyone help me by explaining how the normal mode coordinates are written in Gaussian16 frequency calculations? I understand that they are normalized and hence can be considered "unitless"...
08 March 2023 4,202 3 View
I am trying to apply equal but opposite shear stress to the fixed upper and lower region of the simulation cell. The applied shear will be in the y-direction. Please advice me on the set up and...
07 March 2023 9,805 2 View