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Questions related to Molecular Dynamics
I have a coarse-grain molecular dynamic performed in Gromacs. I am interested, in computing the distance between an atom (bead) and a group of atoms (beads), that we can see as a plane. Thanks...
12 August 2021 6,090 4 View
Hi I am kind of new of 16SrRNA data analysis. I just was wondering if I have metadata with many variables , some of them would be expected to have a stronger influence than others on...
11 August 2021 7,368 4 View
Hello, can you help me interpret these results? It is a 100 ns molecular dynamic of a receptor-ligand complex, red is the ligand. Is there a guide or paper to interpret these results? I really...
10 August 2021 8,949 3 View
I want to parameterize a few molecules. I need of course torsional, dihedral angles, charges , etc. What is the most popular program for that right now? I know that gaussian is quite popular, but...
02 August 2021 161 2 View
Dear all, I have the intention to perform molecular dynamics (MD) simulation of carbon nanotubes (CNT) using Drude polarizable force field implemented in NAMD. Initially, I used CHARMM-GUI to...
25 July 2021 2,056 1 View
Hi MD community: I encountered some problems while generating psf file. As we know, PDB only assumes atom names containing up to 4 characters. However, if the atom name in CHARMM topology is more...
24 July 2021 5,439 1 View
I have generated a complex of antigen and antibody using haddock and used that cluster for MD run using Gromacs. Now I need to find out the inter hydrogen bonds formed between antigen and antibody...
22 July 2021 5,360 3 View
I´m looking for the best configuration to build a workstation to run molecular dynamics simulations of proteins in microseconds. It´s even better with the GPU is compatible with CUDA 11 (NVIDIA).
22 July 2021 5,611 5 View
Hii, I want to know if it is a good choice to do model refinement with online server like 3D refine after model generation instead of Molecular dynamics? I have run the molecule simulations up to...
20 July 2021 1,015 8 View
Hi all, I'm trying to use molecular dynamic simulation to understanding the solvation chemistry of a molecule. I have experimentally determined the density of 0.5 M aqueous solution and I found...
20 July 2021 4,434 3 View
Hello everybody. I'm working with a proteins with oxidase activity that are active when I have it in the cell but lose the activity when I purify it with detergents or polymers. My question if...
16 July 2021 6,721 3 View
Hello! I am wondering if Materials Studio offers a tool to label/count the possible hydrogen bonds in the system? Thanks!
16 July 2021 6,404 0 View
I am currently performing coarse-grained MD simulations in LAMMPS using mW potential for water. I initialize the water model at 273K, equilibrate for 50ns followed by a quenching process from 273K...
15 July 2021 10,061 5 View
Please let me know some free tools for performing MD for the windows platform. I neither have the expertise in Linux operating system nor I can afford paid tool(s).
05 July 2021 1,661 3 View
I performed a minimization simulation of a water box using the tip3p water model in NAMD. The water box was in a sphere of radius 20nm and sphericalBCk1 of 10. The water box changed its shape from...
24 June 2021 9,881 2 View
I am trying to explain the allosteric pathway using molecular dynamics. I have tried to do a contact, correlation and hydrogen bond analysis to determine that path (using holo and apo forms). Is...
22 June 2021 3,893 13 View
I want to study the effect of the length of the polymer chain of PMMA on the complex modulus of the PMMA.
21 June 2021 9,035 1 View
Because, I need the parameters of the Buckingham potential between two similar or different atoms in the simulations of phosphate-based glasses by molecular dynamics, for example, between...
18 June 2021 3,318 7 View
I had a cell that I made a supercell 3,3,3 of it. I did an MD calculation in Lammps, and now I want to see the changes just in the cell that is in 2,2,2 in the matrix of the supercell. How can I...
15 June 2021 8,397 1 View
That is to say the method of synthesis of phosphate-based glass-ceramics doped with Rare Earth Ions.
11 June 2021 3,396 4 View
Dear all. Someone has ever made a calculation of Born Oppenheimer molecular dynamics under the effect of an electric field along a direction.
10 June 2021 8,167 5 View
Dear all, I m looking for a collaborator for performing molecular dynamics of an enzyme and a substrate. Please reply. Thanks Regards, Dinesh S L
07 June 2021 9,142 2 View
Dear colleagues, I have some experience with MD for studies of drug-target interactions, mainly NAMD and Amber. For quite some time, I wanted to try studying the binding/unbinding process of the...
04 June 2021 8,539 3 View
I simulated phosphate-based glasses containing rare-earth ions by molecular dynamics, but when the concentration of rare-earth ions in the phosphate matrix exceeds 8%, the simulation of this...
03 June 2021 1,896 1 View