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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 8,374 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 8,703 3 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 8,422 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 8,561 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 8,672 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 5,167 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 9,256 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 3,177 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 3,139 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 672 5 View
Using Gaussian software, how can I draw Fukui functions (f-, f0, f+)? DFT Simulation, Quantum chemistry, Gaussian,
20 December 2022 8,699 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 7,451 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 463 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 8,639 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 9,749 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 2,780 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 4,017 10 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 2,405 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 4,513 3 View
i will appreciate your positive contributions.
06 December 2022 1,093 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 2,186 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 4,812 2 View
hello, I have a query. I am running 50ns md simulation on GROMACS. I have used CHARMM-GUI for initial file preparation… After that i used following commands for md run gmx grompp -f mdout.mdp -c...
05 December 2022 4,372 4 View
Hello all, I am trying to do equilibrate my sistem. My first trial was done as successful. But my second and third ones are giving this error "Error: an illegal memory access was encountered...
01 December 2022 9,539 0 View