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Questions related to Molecular Dynamics Simulation
My interested thin film compound of study are reported to have optical band gaps from experiments; while my DFT calculations shows half metallic properties. My DFT Optical properties calculations...
02 February 2023 3,526 2 View
How can we investigate the effect of different PH on bio polymers with materials studio? for example with a determined module, like forcite we want to find out what will happen if the PH of the...
01 February 2023 9,879 0 View
If we take a protein or peptide, can we calculate energy without excited in higher stage?
01 February 2023 8,484 2 View
Does anybody know how calculating Interfacial tension (IFT) between two immiscible liquids or liquid/gas in Material studio? Actually, I need to know how to estimate pressure tensors in material...
26 January 2023 5,458 0 View
Our aim is to transfer gene from bacterial plasmid(pET22b) into mammalian expression vector pACGFP1-N1, i have decided restriction sites available in pACGFP1-N1 vector MCS but while doing...
25 January 2023 479 3 View
Dear all I need help on how I use the protein and ligand in the GROMACS and the step I need to do to get the RMSD (the curves) and solvent accessible surface (SASA) analyses) ?
24 January 2023 4,398 3 View
Hello everyone, I want to calculate a ratio, but for some measurements, I have
24 January 2023 9,187 3 View
Good eve. I am afraid of overshooting the pH of hydroxyapatite solution by combining, Ca(OH)2 suspension and phosphoric acid. Can you suggest an acid solution to adjust the pH=10? Recently I...
20 January 2023 2,239 1 View
Hello, I need suggestions of databases, websites or review articles that have number of proteins of unknown structure. Can you guys recommend me any of these approaches so as to identify a number...
20 January 2023 7,842 0 View
In docking studies related articles, pdb id was indicated as for antioxidant, antibacterial, or other activities, but how to cross-verify that the discussed for anti-cancer activity with that...
16 January 2023 388 1 View
There are approx. 1,07,000 atoms in my pdb file and I am trying to replace my atom types according to the forcefield I am using. For example P --->P21 C101 ---> C11 O21 --->...
15 January 2023 9,274 2 View
I'm searching for free software for the QMMM calculations of protein-ligand complexes. Kindly suggest.
14 January 2023 5,921 7 View
I want to build a thin film of BCC iron
13 January 2023 470 3 View
Hello. I am looking far and wide to learn how to simulate my ion channels to understand which of the 5 conformations I got from my cryo-EM experiments are the most stable, and possibly assign the...
11 January 2023 5,181 0 View
Dear all, I am running MD simulation of a protein containing a zinc finger (ZnF) domain. I got its all-atom pdb file and I know there are 4 sulfur atoms in 4 cycteins of ZnF domain interacting...
11 January 2023 8,736 4 View
I just want to know if there is any gromacs command or I have to write a code
08 January 2023 8,609 1 View
Hello, I am running a dft calculation that keeps completing in less than minute giving me this error: "No data on chk file. Error termination via Lnk1e in /apps/gaussian/g16c01/g16/l301.exe" I...
07 January 2023 2,566 2 View
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 8,423 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 8,772 3 View
PEG-6000 is soluble in water but in which compound it changes after its reaction with water?
07 January 2023 6,419 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 8,467 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 8,639 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 8,718 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 5,226 3 View