Roja Rahmani

6 Questions 12 Answers 0 Followers

Questions related from Roja Rahmani

Is it rational to freeze/constraint bond in absence of kb for forcefield parameter?

Hi, I have functionalized Mn-cdS nanotube by amino acid,... . New O-S bond, Mn-O bond,... formed. Now i want to do MD simulation for this functionalized nanotube. (I use AMBER99SB ff) How should...

27 September 2018 2,708 5 View

How make an index for gmx gangle?

Hi, I want to calculate the 1- angle between slab surface plane and water molecule plane 2- angle between OH vector of water and slab plane. How should i define OH vector, HOH plane and surface...

13 September 2018 2,267 0 View

Is there any easier and straight way to make an input for ONIOM method in Gaussian?

Hi, I want to make an input file for using ONIOM method in Gaussian. System contains nanotube functionalized(by amino acid) interacting with a complex protein. when i want to build 3 layer for...

08 July 2018 7,611 4 View

Purpose of using (reflecting) WALL in MD simulations?

Hi, Thre are some articles which use (reflecting)walls(for example carbon walls) in simulation of nanosheet and nanotubes. But i didn't understand the main purpose of using walls in simulation;...

25 May 2018 5,899 6 View

Free evolution and dynamic of amino acid analysis in GROMACS?

Hi, How can i get this analysis in GROMACS? I couldn't get a good result. is it be because of the position restraint that i applied to amino acid? Regards

11 May 2018 9,237 2 View

Is it possible to study the interaction of biomolecules with DEFECTIVE nano tubes with MD simulation by using GROMACS ? does is make a sense?

Is it possible to study the interaction of bio molecules with DEFECTIVE nano tubes with MD simulation by using GROMACS ? does is make a sense? any DFT or quantum calculation should be used or just...

13 March 2018 9,086 5 View