Hi,
How show in ball and stick view by OVITO?
Best
https://ovito.org/manual/particles.modifiers.create_bonds.html
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...
31 December 2018 8,636 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...
31 December 2018 8,557 7 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...
11 December 2018 5,243 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...
10 November 2018 1,644 6 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...
08 September 2018 1,873 6 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...
08 September 2018 5,160 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...
08 September 2018 6,851 7 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
08 September 2018 1,296 5 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...
08 September 2018 3,161 9 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...
08 September 2018 2,414 6 View
How to calculate the RMSD values for a MD simulation using MOE?
07 August 2021 0 0 View
When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.
16 June 2021 0 0 View
Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...
03 March 2021 5,978 5 View
Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...
02 March 2021 2,431 3 View
Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...
02 March 2021 4,910 3 View
Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...
02 March 2021 4,569 4 View
