Molecular Dynamics Simulation

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Questions related to Molecular Dynamics Simulation

Inquiry Regarding Dilatometry Testing of Doped Ceria Ceramics in Indian Research Laboratories?

Dear Researchers, We are seeking to conduct a dilatometry test on a cylindrical green pellet of doped ceria ceramics featuring dimensions of Diameter = 8 mm and Height = 20 mm, encompassing a...

11 January 2024 1,809 1 View

Why is my cloning not working?

I am using a pET28B vector to clone my 2.1kb insert digested with BamH1 (fwd) and Xho1 (rev) restriction enzymes. I'm using over 1ug of DNA for restriction digestion, kept at 37°C for over 3...

10 January 2024 911 4 View

Labile carbon? Refractory carbon?

Is there a way to analyze labile carbon and refractory carbon using an elementar analyzer?

09 January 2024 2,187 3 View

How to define a local coordinate system in ANSYS APDL?

Dear community! I wish my message find you well. I need to simulate rolling wheel and I need to define a local coordinate system at its center to define rotation angle of the wheel about its axis....

08 January 2024 3,536 1 View

Suitable characterization/testing for polymer self healing coating.?

Greeting, in my study I am using reinforced polyester as primer with addition of self healing agent. What should be suitable testing/characterization in order to study the self healing as well the...

03 January 2024 1,697 8 View

How to perform protein-ligand simulation on CYP51 protein with a heme group using gromacs?

Hello, I want to perform 100ns GROMACS simulation using CHARM27 force field on a protein-ligand complex where my protein is CYP51 (PDB ID: 5V5Z) which contains a heme group covalantly bonded to...

27 December 2023 9,212 2 View

How calculate integral of second derivative of Fermi-Dirac distribution function?

If $f_0^0$ is the Fermi-Dirac distribution function, and if the first line of the attached Fig is correct, then is the second line correct? ∂_{a/b} are derivative over $k_x$ and $k_y$. If the...

27 December 2023 6,341 0 View

In Gromacs we have Pull code, is there any code or options related to pushing back the molecule or part of it after pulling it?

In Gromacs we have Pull code, is there any code or options related to pushing back the molecule or part of it after pulling it? I want to see if the conformation or any other structural events...

20 December 2023 7,479 2 View

Nanoparticles in paints?

how we Integer nanoparticles in paints?

15 December 2023 9,423 3 View

Know of any online method for predictions of drug-like ligands for a protein site?

Do you know of any online resource to computationally screen a patch in a protein structure for drug-like ligands?

12 December 2023 8,251 1 View

In LAMMPS, how do you invoke/call the GAP (Gaussian Approximation Potential) machine learning potential function?

I am reaching out to seek assistance in utilizing the GAP machine learning potential that developed 2018 publication titled "Achieving DFT accuracy with a machine-learning interatomic potential:...

07 December 2023 7,562 1 View

Intramolecular bonding calculation from gaussian 16?

Hi all, I have a project to calculate noncovalent bonding interaction. I want to identify if there are any INTRAmolecular interactions in my compound. I was using NCI from Multiwfn to perform it;...

06 December 2023 2,144 5 View

Gromacs distance calculation between multiple atoms, is it real?

Dear all, I have to analyze the trajectory and calculate all distances between a group of atoms (each separate particle) and all the surrounding waters, which were at the distance cutoff

06 December 2023 4,627 0 View

How to remove IgG from mice serum?

I'm measuring serum mice IgE against ovalbumin after 2 IP sensitization followed by 3 intranasal challenges, unfortunately I'm unable to measure the IgE titre due to tge presence of IgG that much...

05 December 2023 1,887 2 View

How do I get the correct enthalpy content for a biomass feed in aspen plus?

I am trying to model a pyrolysis process in Aspen Plus, where the ultimate analysis is as follows: Carbon (C) wt% d.b.: 47.55 Hydrogen (H) wt% d.b.: 6.20 Nitrogen (N) wt% d.b.: 0.07 Sulphur (S)...

04 December 2023 8,840 5 View

"Are scientific journal publications typically paid? Please suggest respected fields for free publication, if available..?

I would like to inquire about the requirement of payment for publishing scientific research papers in international journals. Specifically, I am interested in knowing whether there are fees...

03 December 2023 7,938 2 View

How to generate decoys for validation of generated pharmacophore hypothesis?

Dear all, I have developed a pharmacophore hypothesis using receptor cavity since my protein has no co-crystallized ligand. I , now, aim to validate it using a set of actives and decoys. I tried...

01 December 2023 1,374 0 View

Have gravitational forces been invoked to explain the fracture of large blocks of stone into two parts?

The motivation comes from the following common observation. Blocks of stone with large dimensions (say of the order of three meters or larger) can be easily fractured into two pieces. First,...

29 November 2023 5,248 2 View

Why did I observe more than one band in my PCR product?

What is your solution regarding extra bands in ITS molecular markers? I am trying to use ITS1 and ITS4 markers in 15 plant species. Unfortunately, I only received extra bands instead of one after...

29 November 2023 9,256 4 View

Which compuational tool can be used for protein protein docking if prtein has non standard amino acids?

one of the proteins I am trying to dock has a phosphorylation at one of the residues and i want to dock it , without changing that residue, which tool can be used for such non standard, post...

28 November 2023 5,653 1 View

What is the cause of failure in TS calculation of gaussian?

Hello. Sorry for asking this question in poor English. I am a student studying organometallic chemistry. I am doing a TS calculation using gaussian16 to find a pathway for a catalytic reaction,...

27 November 2023 4,001 6 View

Do you measure the pitch length of chiral nematics in your lab? Is measuring the distance between two lines in the fingerprint texture reliable?

Hi, I would like to seek advice/collaboration with anyone who measures the helical twisting power of chiral nematic liquid crystals. I would like to contact you directly.

27 November 2023 1,975 4 View

In MD simulation, is it possible to move all atoms simultaneously in each step?

Hi everyone, As you know, in MD simulation of a biological system, typically, one atom is moved, followed by recalculating forced, then another atom is moved and so forth. Do you know if any of...

25 November 2023 9,718 2 View

How to use LAMMPS to calculate the vibrational frequencies of systems with interstitials?

I am currently engaged in calculating the phonon vibration frequencies of self-interstitial atom (SIA) clusters in tungsten, aiming to subsequently compute the vibrational free energy.Due to the...

25 November 2023 7,939 1 View

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