Alireza Sadeghifar

6 Questions 7 Answers 0 Followers

Questions related from Alireza Sadeghifar

Surface Tension_ Molecular Dynamics?

Hi Everyone, I'm trying to calculate the surface tension tail correction in Molecular Dynamics. Is there a method to integrate the equation suggested by Chapela et. al (Computer simulation of a...

06 April 2023 3,622 0 View

How to obtain/visualize the orbitals in ONIOM calculations (QM/MM) using DFT methods?

Hello everyone, I am doing a single point calculation on my system using ONIOM (QM/MM). The checkpoint file (and also formatted chk), which is generated from this calculation does not show any of...

01 October 2017 9,915 4 View

How to add counter-ions to a charged protein to neutralize it? (Gaussian)

Hello everyone, I have a protein system (complex with a substrate) with a total charge of -9 (the charge of the ligand is -5 and the protein is -4). I want to do some QM/MM calculations using PM6...

22 June 2017 7,600 5 View

When (how) does one use (do) the reflective boundary condition in molecular simulations?

Hello everyone, I am doing NVT ensemble Monte Carlo simulations for adsorption on surfaces and my question is when one uses the reflective boundary conditions in this ensemble? And how is it done?...

06 June 2017 4,919 4 View

Where and when is the rotation of the axis of quantization allowed? Is it system dependent or planet dependent (or something more complicated)?

We are working on a project including the rotation of the axis of quantization in molecular simulations. To put it simply, we have a system in which the H2 molecules in the gas phase are in...

21 April 2017 5,149 22 View

How do I visualize para, helicoptering and cartwheeling ortho quantum hydrogen molecules on a surface?

I have a bunch of hydrogen molecules adsorbed on an ionic surface. The hydrogen molecules present on the surface are only the ones with angular momentum J=0 { |Mj|=0 }, and J=1 { |Mj|=0,1 }, i.e.,...

28 April 2015 6,599 1 View