Contact experts in Molecular Dynamics Simulation to get answers
1,876 views 2,936 posts
Questions related to Molecular Dynamics Simulation
Kindly help
16 September 2022 4,041 0 View
I'm constructing a phylogenetic tree using microsatellite sequences in MEGA11. I have aligned the sequences using MUSCLE and now I can see a lot of "xxx" and gaps in many of the sequences. Kindly...
14 September 2022 6,515 3 View
I want to output the length of the crack in real time in the simulation of lammps
30 August 2022 2,814 4 View
I have installed the GROMACS in Windows Subsystem for Linux - Ubuntu. The simulation is working perfectly on the CPU and I am unable to run it on GPU. I realized that the GPU is disabled as per...
22 August 2022 7,193 2 View
The table bond_style doesn't allow us to tabulate the parameters of the bond_coeff for a particular bond_style. Is there any way to read in values for 1000 distinct bond_types instead of having to...
11 August 2022 2,078 0 View
How to includes the M062X functional in the Gaussian 09 ?
06 August 2022 3,374 4 View
I wanted to perform simulation of methanol by including oplsaa forcefield and methanol.itp file. But when I run gmx solvate there is an error called " methanol.gro file not found in current...
22 July 2022 6,086 0 View
Hello Everyone, I have performed an enhanced sampling molecular dynamics simulation for the dissociation of ligand from a protein-ligand complex and generated the "Potential of mean forces"...
19 July 2022 3,183 2 View
I want to learn graphic design related to biological science. Please recommend me a course or software.
02 July 2022 8,517 7 View
I've been trying to run some phonon dispersion calculations and I cannot get the matdyn.x routine to work. I've tried several different tutorials, but none work. Currently I'm using quantun...
10 June 2022 569 1 View
I was doing a md simulation by using lammps, and when i run lammps, i met the problem below, which i cannot find the error code in official website of lammps. Does anyone know which kind of error...
24 May 2022 9,669 1 View
I have been using QwikMD/NAMD to run MD simulations, and for each setup I run three simulations to have replicate results. Now, I would like to plot the results from the three trajectories, along...
19 May 2022 4,827 3 View
Every time I start loading a lammps dump file of more than 4GB in windows, VMD crashes. Are there any certain modifications I need to make?
15 May 2022 8,880 4 View
I wanted to start the molecular dynamics simulation of a couple of ligands. Selecting a forcefield has been a difficult to do, for me. I was hoping to the ResearchGate community could help me.
10 May 2022 2,741 1 View
I am trying to run Vina-Carb to dock malto-oligosaccharides in enzymes, but the vina-carb does not start correctly and I suspect it is due to the nomenclature in the ligand .pdbqt file. What is...
03 May 2022 6,241 0 View
I am docking three ligands with more than one proteins. Two of the ligands are already approved drugs and third is a plant compound. My all ligands accepts gasteiger charges and docking went...
30 April 2022 9,836 3 View
I have done MD simulation and want to interpret and plot the data from the files. As my PC did not have enough specs for Dual boot OS because the XmGrace tool is supported only on Linux. Though, I...
26 April 2022 4,203 3 View
After performing Molecular Docking between Protein-ligand complex in Autodock vina, how do we validate the results to be accepted? Is Molecular Dynamic Simulation help in doing so? Please provide...
25 April 2022 2,962 12 View
Suppose you do de novo assembly of a mammalian genome. How do you calculate the N50 value? I have tried quast but its fails probably because of the huge size of the genome.
22 April 2022 5,024 5 View
Can someone please help me with a protocol for parameterizing a metallo-protein for MD simulation with amber forcefield? My protein has two FE molecules and the I tried using either...
20 April 2022 4,448 1 View
We used the MEAM potential to investigate the melting and solidification process on a cube of a specific alloy. Heating to a temperature sufficiently above the melting point was performed at a...
17 April 2022 5,977 2 View
I have run REMD (replica exchange molecular dynamic) simulations of a dimer. I want to do 3 different types of clustering based on: 1. The RMSD (Root Mean Square Distance) between chain A and...
06 April 2022 5,973 2 View
I have completed the md simulation of protein ligand complex using Gromacs I am a newbie to gromacs .. Linux, but executed successfully. I would be grateful if someone could help me out. Thank...
22 March 2022 696 6 View
Hello I did 100 ns simulation using GROMACS a protein protein complex ( chain A for antigen - chain B & C for antibody) now I want to calculate the number of hydrogen bonds. I select chain A and...
18 March 2022 628 5 View