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Questions related to Molecular Dynamics
Hello, Can anyone inform me on the techniques (other than semi grand canonical or grand canonical ensembles) that one can use to calculate the equilibrium impurity (say P) concentration in...
22 November 2019 5,277 3 View
I am working on some more complex membrane simulations and wanted to know if there is a specific advantage to using a certain ensemble. It seems as though most people have used either NVE, NVT, or...
21 November 2019 1,379 3 View
I have a membrane-protein system prepared using CHARMM-GUI. Now, I want to place some ions near the protein towards the extracellular side, intracellular side and inside the protein as three...
11 November 2019 3,678 10 View
Dear experts, I am trying to match the spontaneous polarization value of BaTiO3 using PBE functional from the following paper -...
11 November 2019 8,731 9 View
Hi, There are many journals related to simulation that used Silicon cluster as the substrate model. I have also seen SiO2 cluster model on the research journal. However i can't seem to find any...
08 November 2019 8,287 1 View
Hi. I have a doubt regarding Molecular Dynamics (MD) and Brownian Dynamics (BD). What is the criteria that is used during the evolution of the equation of motion in both MD and BD that ensures...
05 November 2019 5,760 4 View
Hello everyone, I'm having an issue with a review of a paper. I performed 50ns MD simulations on docking poses to know if the predicted poses were stable. Among the literature doing similar...
25 October 2019 4,737 5 View
I am working on computationally understanding the active and inactive conformations of some proteins. Simulating the inactive conformation from the active conformation is reported in literature by...
23 October 2019 5,870 2 View
I want to obtain some protein's open/closed states without using Molecular Dynamics, so is there exists some python scripts to realize my goal? Thank you very much!
11 October 2019 3,360 3 View
I have been trying to run psfgen for a protein in question (albumin) and a ligand (diisocyanate) from a docking pose. I have parameterized my ligand with CGenFF and downloaded the CHARMM topology...
03 October 2019 9,500 2 View
I have prepared a rectangular amorphous carbon (a-C) sample using molecular dynamics (LAMMPS) simulation. How can I measure the partial charges in each atom of this large system having ~20,000...
09 September 2019 1,253 11 View
How can I use Lammps and ReaxFF to determine the Arrhenius rate constants for chemical reactions? I can't seem to find a straightforward tutorial/code for this specific task.
09 September 2019 9,364 15 View
I am working on cyclodextrin inclusion complexes and find out their geometries,particularly the orientation of the guest in the cavity. Which computational method out of DFT, MM and MD would...
07 September 2019 1,307 6 View
I want to calculate specific surface energy of [111] surface of Nickel. Code: units metal dimensions 3 boundary p p p atom_style atomic lattice fcc 3.52 orient x -1 -1 2 orient y 1 -1 0 orient z 1...
04 September 2019 9,862 3 View
Dear all, How do you find the melting point of a material using the two-phase method with DFT+MD? Thanks, Uthpala
03 September 2019 9,751 6 View
I am simulating electroporation in varying cholesterol content in the lipid membrane. I am trying to simulate each system exactly in the same conditions and with the same protocols, but the system...
18 August 2019 3,160 5 View
Dear colleagues, I try to perform MD simulation of abstract polymer in good solvent. Particularly I try to calculate solution viscosity by means of non-equilibrium dynamics (shearing). Although...
17 August 2019 10,009 2 View
So i have two structures, both ligand bound, and i need to predict the structure of the ligand free molecule. To my knowledge it is not possible but i am quite at the beginning of understanding...
12 August 2019 7,243 2 View
Contact angles are usually determined by goniometry. However, more often than not, this method reveals apparent contact angle (which reflects the net effect of surface chemistry and surface...
30 July 2019 8,421 6 View
I am performing a molecular dynamics simulation from CRBN protein (PDB ID: 4tz4), which contain a ZN binding site composed of four cysteines. The main goal is understanding the chemical and...
22 July 2019 8,238 3 View
So i have my two proteins and a protein linker all in PDB format. I need to combine them in as precise as possible way. What software would you suggest me to use? The orientation is not the most...
10 July 2019 6,791 4 View
I created .prmtop topology and .inpcrd coordinate files in tleap, and then I ran minimization, heating, and equilibration steps, and then 10 ns of production with pmemd in AMBER 14 and created...
05 July 2019 3,334 3 View
I have a nucleic acid that has bad termini. I can use Swiss Pdb viewer to reconstruct it but i wondered what is the most precise tool for it? Gromacs has no function to do that and charmm36 does...
24 June 2019 2,678 3 View
My protein and inhibitors, give different trends in MST data. Fnorm either it is in upward trend or downward trend. What does that mean ? can we define the inhibition level or the pattern with...
27 May 2019 5,743 1 View