Which one is better? AMBER or UFF?

More Roja Rahmani's questions See All

How show box in CHIMERA?

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

What is the difference between surface and bulk solution? Which one is more polar?

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

How show in ball and stick view by OVITO?

Hi, How show in ball and stick view by OVITO? Best

31 December 2018 8,262 1 View

Problems with g_dist?

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

How calculate adsorption number of molecule in molecular dynamics simulation?

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

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...

08 September 2018 1,873 6 View

How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

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

How can i calculate the distribution of water polarization above surface?

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

How define Mn in AMBER forcefield?

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

How functionalize ZnS nanotubes with different organic and inorganic molecules?

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

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

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

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

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

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

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

How to repeat an operation on an atom selection for multiple times in PyMol?

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

What is the characteristic length to determine the Reynolds number for the scattered turbulent fluid flow?

Dear all, I just saw this example in FB on the difference between laminar flow and turbulent flow. The flow from a pipe hits the sink and scattered. The flow from the pipe is characterized as...

02 March 2021 1,999 5 View