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Questions related to Molecular Dynamics
I need a way to rotate my entire system (DNA and solvent) such that the axis of the DNA lies along the x-axis, but I want the periodic boundaries to be preserved. I added pictures of my system...
01 June 2021 7,282 3 View
I am beginner using Material studio for Performing Molecular dynamics, I am getting stuck in modeling of MWCNT exactly at the centre of an amorphous cell. I am attaching an image below for...
31 May 2021 1,728 3 View
Hello, so far i've come across lots of papers using conventional MD to study stability of protein-ligand binding after molecular docking. What i am curious is, could accelerated MD be used for...
28 May 2021 7,712 3 View
Is there any change that needs to be made to the mdp available in the g_mmpbsa tutorial to calculate the free energy binding of a coarse-grained system (my system is a discoidal lipoprotein) or...
23 May 2021 3,627 0 View
Interaction of residues during molecular dynamics
22 May 2021 9,710 3 View
Hi I have been trying to optimize well-tempered metadynamics simulation in Gromacs 2020.4 engine using plumed, on a transporter from Major Facilitator Superfamily. I have the existing structure...
22 May 2021 3,668 2 View
Hi everyone! The said fatal error stopped my run altogether. It did, however, started minimization. Any idea how to solve this? Thank you so much!
20 May 2021 4,557 1 View
Hi everyone! I'm doing an MD run on Gromacs on HPC and the error attached below popped up. The original rlist was 1.2, and I tried decreasing it to 1, then 0.5, then 0.1, but the same error still...
19 May 2021 2,973 3 View
I have a VASP MD simulation of a 2x2x1 supercell of Al2O3 totaling 120 atoms. The supercell was initially relaxed and then run for 1500 time steps (0.1 fs time step, 1e-7 EDIFF) in the NVE...
18 May 2021 3,550 2 View
Presently we measured the nonlinear response of an organic compound using the Z-scan method. The magnitude of the nonlinear refractive index of the compound solution was found to be negative at a...
10 May 2021 1,841 7 View
Please, I sincerely (and urgently) need a suggestion on any reliable free Online tool for Molecular Dynamics (MD) Simulation. I need it to generate RMSD plot for a protein-ligand binding study I'm...
30 April 2021 1,174 5 View
What is the best version of gromacs software to accomplish molecular dynamics?
29 April 2021 3,492 3 View
For a dense gas, the time constant is determined by fitting an exponential decaying function to the velocity autocorrelation function of an MD simulation, but what form is used for liquid VACFs...
23 April 2021 5,490 3 View
Hey guys, I did the docking using the molegro, and now I need to perform the molecular dynamics of my best pose and my protein. I'm using Namd to do this, my question is: first of all do I need...
22 April 2021 982 1 View
Hi, For quite a long time I've been trying to simulate polyphosphate ester molecules using GROMACS software with topology generated with Acpype, but with little success. The first approach...
17 April 2021 794 2 View
Hi, I'm working on Gromacs on HPC to run MD simulations. I tried combining individual files from step 5, which is the MD production step, using the gmx trjcat command so that I could post-process...
15 April 2021 1,638 2 View
Hi, I was wondering which topology generation tool is more suitable for various small organic solvent molecules (which dissolves a solute). From my understanding, TPPMKTOP matchs the atoms to the...
09 April 2021 2,713 1 View
How could we relate the experimental ic50 values of ligand molecules with in-silico binding stability results? A molecules which have a low IC50 (experimental) having high binding stability...
09 April 2021 2,725 1 View
I have created an Ice 1h structure and created an adhesive bond with the substrate in LAMMPS. Now in order to replicate an adhesion test, I need to detach it using a tensile force that pulls it...
07 April 2021 2,976 2 View
Hello, I was wondering if you could recommend any libraries for MD simulations of proteins with ligands in Python. They may also be accessible via bash. They need to be available for free in...
29 March 2021 6,044 5 View
I want to draw a schematic diagram of the different structures of PVDF, but when I import the CIF document into Material Studio or Diamond, I find that the positions and bonds of the atoms are...
29 March 2021 2,737 2 View
I have a pre-equilibrated Ice 1h structure at 250K. I also have an Aluminium substrate which is 10 Angstroms below it within a simulation box. With the potential defined for structures (TIP4P for...
19 March 2021 8,695 4 View
In brief, the first protein-ligand complex I generated was by using AutoDockVina and the second protein-ligand complex I generated was by using the HADDOCK web server. Therefore, is there a way I...
16 March 2021 6,395 5 View
Dear researchers, I am new to Molecular dynamics. I would like to do protein-ligand molecular dynamics by using gromacs. My ligand is goniothalamin and my protein is PDB id 2c56 protein. I...
15 March 2021 1,883 11 View