23 Questions 37 Answers 0 Followers
Questions related from Roja Rahmani
Hi, I did an MD simulation by gromacs and now I want to show it in CHIMERA. As CHIMERA can not read a .gro file, I converted it to .pdb but I can't see the simulation box. How can I see the...
01 January 2019 9,215 2 View
Hi, What is the difference between surface and bulk solution? Which one is more polar? does it depend on the characteristic of surface? Since ZnS surface(nano sheet) is partly hydrophobic, so...
01 January 2019 8,740 7 View
Hi, How show in ball and stick view by OVITO? Best
01 January 2019 8,619 1 View
Hi, my system contains 30 same molecule around nanotube. each molecule is in 2nm far from nanotube. i want to know how this distance change during simulation time. I have attached the same...
12 December 2018 5,361 1 View
Hi, My system contains 20 amino acids around nanotube. I want to know the adsorption amount of AA DURING simulation time; the adsorption occurs when the distance between one of non-hydrogen atoms...
11 November 2018 1,802 6 View
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...
09 September 2018 8,088 1 View
Hi, There are many studies about functionalizing different ZnS nanostructures. but i couldn't find anything about ZnS nanotube. Is it possible, at all? would you please share me your...
09 September 2018 3,269 9 View
Hi, How can i calculate the angular distribution of the angles between water molecule water and surface? surface during molecular dynamics simulation? I did simulations by GROMACS, is it...
09 September 2018 5,304 3 View
Hi, I study the interaction(calculating PMF for different distances of molecule above surface) of amino acid with surface in presence of water( using TIP3P water model, AMBER force field by...
09 September 2018 7,006 7 View
Hi, I do molecular dynamics simulations and new in quantum calculations. Recently i studied the interaction of amino acid with ZnS nanotube by DMOL3 and i wanted to know that does any bond formed...
09 September 2018 2,533 6 View
Hi, I have Mn in my strucrure and i want to use AMBER forcefield in GROMACS. But it is not defined in atomtypes. What should i do exactly? Best regards
09 September 2018 1,401 5 View
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...
09 September 2018 1,990 6 View
Hi, I want to study the interaction of functionalized(by amino acid)inorganic nanotube with protein using QM/MM calculations. The nanotube has 150 atoms. I functionalized it by aminoacid by DMOL3...
08 August 2018 7,667 10 View
Hi, I am a student and need high processing computers(cluster) for quantum calculations. Would you please introduce me any website which i can use their computers freely?
07 July 2018 2,372 5 View
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...
07 July 2018 4,439 6 View
I want to study the interaction of protein with functionalized nanotube by QM/MM calculations. Would you please introduce me some user friendly and accurate packages for this purpose(exceot...
07 July 2018 3,430 2 View
Hi, I use ONIOM method( in gaussian) to study the interaction of protein with nanotube. I uss UFF force field for low level(for protein). Is UFF an accurate forcrfield for this means or AMBER is...
07 July 2018 5,669 3 View
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
05 May 2018 3,604 2 View
Hi, I want to functionalize Sulfur contained nano tube with sulfur contained amino acid and i want to study the interaction of moleculeswith this functionalized nano tube. I use GROMACS for...
05 May 2018 7,416 0 View
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;...
05 May 2018 1,742 7 View
Hi, How this property can be calculated in GROMACS? By which tool? Regards
05 May 2018 6,453 3 View
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...
03 March 2018 3,569 6 View
I am beginner user of GROMACS. i need a specific tutorial to help me through it
10 October 2017 3,000 7 View
