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Questions related to Molecular Dynamics Simulation
I was wondering if someone could clear up the difference between domain decomposition in GROMACS and LAMMPS. As I understand it LAMMPS creates ghost atom copies of atoms in surrounding domains and...
08 February 2023 9,013 0 View
Hello! I have performed umbrella sampling to study the covalent bond formation between a ligand and a Cysteine residue. Where Histidine is a proton-donating residue to complete a reaction. I have...
08 February 2023 4,791 1 View
I am adding the Graph result below. The whole trajectory run was 20 ns. is there any particular threshold value for H-bond?
08 February 2023 9,359 2 View
sir/madam can anyone suggest the physical unit of Fukui function in Density functional theory calculations
08 February 2023 3,810 2 View
If estrogen is not exogenously given, can MCF7 cells grow into tumors under the skin of female nude mice?
07 February 2023 9,964 2 View
I want to determine the interaction energy between the MgO surface and polymer coating using Materials Studio software. What should be (h k l) cleave plane to have a cut-off distance of at least...
06 February 2023 6,318 1 View
Dear all, I am currently working on the simulation study of a complex whose ligand cannot be automatically parameterized. I have been using AMBER to do the parameterization, and now I have...
03 February 2023 317 2 View
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 3,448 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 9,821 0 View
If we take a protein or peptide, can we calculate energy without excited in higher stage?
01 February 2023 8,428 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 5,409 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 423 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 4,339 3 View
Hello everyone, I want to calculate a ratio, but for some measurements, I have
24 January 2023 9,131 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 2,173 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 7,778 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 341 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 9,215 2 View
I'm searching for free software for the QMMM calculations of protein-ligand complexes. Kindly suggest.
14 January 2023 5,865 7 View
I want to build a thin film of BCC iron
13 January 2023 422 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 5,136 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 8,669 4 View
I just want to know if there is any gromacs command or I have to write a code
08 January 2023 8,545 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 2,511 2 View