Kang Hu

6 Questions 15 Answers 0 Followers

Questions related from Kang Hu

How to calculate the rotational kinetic energy of single water molecule im MD?

Hi All, I have a quick question about the rotational kinetic energy of single water molecule. I tried to extract that of a single pure water molecule by 'gmx traj -ekr' in GROMACS. Surprisingly,...

21 January 2022 9,740 4 View

How to calculate the energy/strength of the Hodrogen Bond by MD?

There are several different definitions of H-Bond (geometric crieteria, and a combination of geometric and energetic), but It seems that there is no way to estimate the strength for a target...

11 November 2021 8,687 2 View

How to extract the electrostatic force that a target water molecule experienced with GROMACS?

Hi all! I have performed the MD simulation on aqueous lysozyme solution(withou external electric field) with GROMACS. Q1: Is there any way to extract the electrostatic force that water...

05 August 2021 6,452 2 View

How to get the internal electrostatic force field of protein solution with MD simulation?

Hi all! I have performed the MD simulation on aqueous lysozyme solution(withou external electric field) with GROMACS. Now, I want to map the spatial distribution of internal electrostatic force...

15 June 2021 1,707 1 View

MD simulation of highly concentrated protein solutions with GROMACS?

I am trying to bulid a dense aqueous Lysozyme sysytem by GROMACS. First, I creat a cubic box with side length of 8.7 nm. Then, I put several lysozyme molecules into the box with command...

11 March 2021 6,754 11 View

How to put two different proteins(or 1 protein molecule and 1 sugar molecule) in one box for MD simulation with GROMACS?

I am tying to simulate the water dynamics in the preservative solutions including two protective agents, trehalose and ε-poly-L-lysine.So I need to put these two diffenernt molecules in one single...

01 December 2020 2,349 3 View