Molecular Dynamics Simulation

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Questions related to Molecular Dynamics Simulation

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 7,571 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 2,159 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 4,641 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 1,895 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 8,850 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 7,947 2 View

The image attached is the anatomical section of Cephalandra. Could someone please help me to identify? the large lignified cell present within phloem?

The cells mentioned here is present both in outer and inner phloem

02 December 2023 4,132 1 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 1,383 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 5,254 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 9,265 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 5,665 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 4,011 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 1,988 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 9,726 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 7,947 1 View

What is the differences between bioactive compounds and pharmacological actions?

what is the differences between bioactive compounds and pharmacological actions?

21 November 2023 2,281 1 View

Do you agree that physics picks out entities and definitions that satisfy it?

Also called the conventionalist interpretation of physics success this is a main counterargument against the ni-miracles thesis i.e physics success cannot attributes to biz are epistemology or...

20 November 2023 9,283 2 View

Docking using QM charges?

I did some docking using autodock4 and used QM charges (derived at b3lyp/6-311++g** level) into my ligand's *.pdbqt file (manually); but the docking scores instead of improving gotten worse. Any...

18 November 2023 2,288 2 View

How to analyze and validate docking procedure for a protein with no co-crystallized ligand ?

I'm working with a protein that does not have a co-crystallized ligand. How to analyze the best docking pose and validate the docking procedure?

15 November 2023 2,008 2 View

How i can address this reviewer feedback in my article?

i submitted my article in where i conducted molecular dynamic simulation 100 ns for a complex protein-ligand. Reviewer asked us for more work to be done for this study as below ''More extensive...

14 November 2023 4,552 1 View

How to generate ligand.itp and ligand.gro files for md simulation using amber14 force field?

How to generate ligand.itp and ligand.gro files for md simulation using amber14 force field?? Kindly help!! Thanks in advance.

13 November 2023 2,407 4 View

Can artificial intelligence replace future architects?

With artificial progress, is there any need for designers and architects anymore? In your opinion, in which parts can artificial intelligence be replaced and in which part designers and...

12 November 2023 5,051 3 View

XRD METALLIC GLASSES. Phases in Zr-Cu-Al-Fe amorphous metal after hpt process ?

Dear colleagues. I am trying to determine the phase composition of an amorphous metal after intense plastic deformation and after annealing at the peak temperature on the DSC curve. Unfortunately,...

08 November 2023 8,317 0 View

Can the results of molecular docking be justified without md simulations?

The molecular docking was performed by redocking the co-crystallized ligand and validating the protocol by finding the RMSD of the docked ligand by superimposing it on co-crystalized ligand....

05 November 2023 6,503 4 View

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