How can I get Simulaton Box Angle over the Simulation time Period ?

More Juganta K Roy's questions See All

How can I quantify the water molecules diffused in the Polymer network?

I want to calculate the number of water molecules diffused around the polymer-water interface as well as in the bulk polymer. In my case, the x-direction length is decreasing. I tried with...

06 July 2014 4,447 10 View

Can I use g_denstiy in case of NPT simulation system?

Dear gmx Users, I want to use g_density to characterize the interface of water-polymer in case of NPT simulation by using both mass and number density in gromacs-4.6.5. But when I googled, I got...

06 July 2014 526 4 View

What is the required time for NVT and NPT equilibration?

Dear All, I am doing simulation of an epoxy polymer and water system in gromacs using charmm27 forcefield. I got required temperature (300K) in NVT after 500 ps simulation and in NPT 30 ns...

05 June 2014 4,704 4 View

Atomtype OWT3 not found

I am a new user of GOMACS. My system contains Polymer and Water. I used gromos53a6 force field and spc water model and it ran nicely. But now I want to use TIP3P water model with the same force...

06 July 2013 4,584 11 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

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

What is your perception on using visual analysis or quantitative approaches to evaluate data from single-case research designs (n of 1 trials)?

Results of single-case research designs (i.e., n-of-1 trials) are often evaluated by visually inspecting the time-series graph and computing quantitative indices. A question our research team is...

03 March 2021 687 1 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

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

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

Why the results when using wall thickness and when using shell conduction are different in ansys fluent?

Actually, I am running cfd simulation for a heat exchanger which has two fluids one hot and other one is cold fluid. there is a solid domain between them, which I removed and instead I have used...

01 March 2021 9,537 2 View

Joint behaviour in Abaqus is not captured well?

I am working on roof joint and trying to simulate the behaviour in Abaqus. I am successful in running the model but the final graph does not follow the experimental curve in the negative direction...

01 March 2021 6,661 3 View

Justin Lemkul

The box angles don't change over time, so they are the same as whatever they were set to when defining the box with editconf.

Juganta K Roy

Thanks Justin for your suggestion. So, even if I do simulation with anisotropic pressure coupling, the box angle will be same as before?

Dear Justin,

I did NPT md simulation for 164 ns and got the box vectors by using g_traj. I calculate the angle between b and c; which is changing (slightly) over the simulation period. I have attached the graph (obtain by Mathematica). Would you please tell me this change is ok or not?

Thanks