Ehsan Shahini

9 Questions 7 Answers 0 Followers

Questions related from Ehsan Shahini

Can we relate the zeta potential (from experiment) to the total charge of a molecule in molecular dynamics simulation?

I have the experimental result for the zeta potential of a (g-C3N4) nanosheet, now can I relate that to the total charge of a molecule to be used in a molecular dynamics simulation?

01 April 2022 652 2 View

How to get the enthalpic change of solvation of a small molecule in a solvent in molecular dynamics simulation?

I did a free energy calculation based on the BAR method (in GROMACS) and now I want to see the entropic and enthalpic contribution of that free energy. How could it be done with molecular...

27 February 2022 9,189 2 View

Is it possible that a hydrogen bond length be around 1.26 Å?

I have a mixture of DMF and water in 300 K simulated with an OPLS-AA force field. The hydrogen bonds between oxygen atoms of DMF and H atoms of water have a very short length and it's around 1.26...

22 November 2021 2,664 3 View

What the van der Waals and Coulombic terms can tell us in a solvation free energy calculation?

I have calculated the solvation free energy of two graphitic carbon nitride sheets (g-C3N4) of different sizes and the results are shown in the figure below. 1. My question is why for the...

18 August 2021 5,592 4 View

Is there any database for organic solvents that we can get their properties in datasheet?

I need a database of organic solvents with some of their properties such as "density", "isothermal compressibility", "surface tension", "enthalpy of vaporization", and "dielectric constant". Can...

09 August 2021 4,090 4 View

Does the calculation of PMF depend on the path of the reaction coordinate?

I have a fundamental question about the Potential of Mean Force (PMF). Does this quantity a path-dependent value or not? Let’s say we have two graphene sheets stacked on each other (see Figer...

31 March 2021 474 4 View

How to get the solvent density profile from an Molecular Dynamics trajectory file?

I want the density profile of a solvent in a particular direction when we have the trajectory file from molecular dynamics simulation. For example, analyzing the solvent density around a protein...

12 January 2021 7,847 3 View

How to get the bond length and bond angle distribution for a molecule from molecular simulation results?

I have a g-C3N4 sheet and I want to know the probability of bond length and bond angles for this material (something like the attached photo) from its trajectory result. Is there any specific...

24 June 2020 9,084 6 View

What is the best programming language as a tool to investigate the mechanical properties of nanomaterials?

I am working on mechanical properties of nanomaterials using Molecular Dynamics simulation. I am familiar with MATLAB as well as C++ and Python. However I want to improve my skills but I am not...

27 March 2018 5,634 4 View