Contact experts in Molecular Dynamics Simulation to get answers
2,218 views 3,179 posts
Questions related to Molecular Dynamics Simulation
I optimized endohedral fullerene Li@C20 using DFT/B3LYP in Gaussian 09. 6-31G++(d,p) basis set was used in calculations. Total energy of structure is correct and there is the same information in...
07 January 2023 8,379 8 View
Dear all, I want to compare the reactivity of two diastereomers in a reaction, and therefore I'd like to calculate the activation energies of two compounds in a rate-limiting step. I've optimized...
07 January 2023 8,712 3 View
PEG-6000 is soluble in water but in which compound it changes after its reaction with water?
07 January 2023 6,347 1 View
I was trying to run receptor grid generation. After I clicked on "run" tab, the mentioned error occurred and I couldn’t start docking process. I’d like to ask for your assistance in this case....
06 January 2023 8,429 3 View
After the protein structure prediction using AlphaFold2, I want to proceed with molecular docking in Autodock. However, the modelled protein structure cannot be opened using Autodock with the...
04 January 2023 8,574 10 View
Dear all, I am running eABF simulations using CHARMM36 additive FF in NAMD for a few systems with water. The relevant input parameters are added below. cutoff 12.0;...
23 December 2022 8,677 4 View
Hi! I would like you to help me with information about full predoctoral or PhD fellowships in bioinformatics, if possible in the area of microbiology. Thanks Fausto Cabezas-Mera
23 December 2022 5,172 3 View
I want to use the lanl2z basis set for Pt and the rest molecule with 6-31gd # avogadro generated ORCA input file # Basic Mode # %pal nprocs 6 end %maxcore 2000 %basis "6-31g(d)" # All...
23 December 2022 9,264 6 View
Plagiarism report is an important for any research article. Which one is better, free and available to give report? Please specify if any
22 December 2022 3,184 4 View
Running MD simulation , NVT equilibrium, on google colab , some restarts are required due to time limitation of the server. I wonder if there is a way to find out how many steps are left to...
20 December 2022 3,149 2 View
Hi, guys. I started doing some dockings a few days ago and there was an constantly error showing up on the autodocktools cmd: "swig/python detected a memory leak of type 'BHtree *', no destructor...
20 December 2022 680 5 View
Using Gaussian software, how can I draw Fukui functions (f-, f0, f+)? DFT Simulation, Quantum chemistry, Gaussian,
20 December 2022 8,710 3 View
How to detect Antibiotic and heavy metals at the same time by using Uv-Vis spectrophotometry? The sample is soil leachate
19 December 2022 7,461 3 View
Hello everyone. I'm new to molecular dynamics and don't have enough knowledge of LAMMPS. I want to do a tensile test of graphene - GaN nanosheet. I have the data file of the sheet and I'm using...
18 December 2022 470 3 View
gmx mdrun -deffnm nvt Back Off! I just backed up nvt.log to ./#nvt.log.1# Compiled SIMD: SSE4.1, but for this host/run AVX2_256 might be better (see log). Reading file nvt.tpr, VERSION...
16 December 2022 8,646 1 View
Dear Experts I am using AutoDock 4.2.6 in my desktop since 2 years. However, from an unknown reason, it gave up working last week. When I click on the AutoDock Tools 1.5.6 icon on the desktop,...
15 December 2022 9,760 3 View
If i want to sett the mass of ligand like 50 ng/ml. How to do it? Im using gromacs for simulations
13 December 2022 2,786 5 View
In order to calculate LUMO and HOMO levels for an organic substance, I need to determine the onset Potential (oxidation and reduction). How to do it with the attached picture? Thanx in advance.
11 December 2022 4,026 10 View
Hi everyone. It is known that all Si-SiO2 wafers absorb the liquids around them due to their low hydrophobic properties. For some nanofabrication purposes, it is critical to have a sample free...
09 December 2022 8,065 1 View
I have simulated my viral protein at a temperature of 300K (room temperature). However, it does not seem to stabilize even after 400 ns of simulation. I have observed many papers where simulation...
08 December 2022 2,412 2 View
i was building the 3D QSAR, but q square 0.9, is there any way to validate the QSAR, so that value of q square can > 0,5?
06 December 2022 4,519 3 View
i will appreciate your positive contributions.
06 December 2022 1,100 0 View
Hello! I have some transcriptome data in .pep format I need to blast against. I was wondering How I can convert .pep files to .fasta? Best Hanna
05 December 2022 2,192 1 View
We are looking for a bioinformatician who can help us with AI based deep docking system or you can provide us a training programm to learn such a art of bioinformatics.
05 December 2022 4,819 2 View