How can temperature setting differ while running NVT from NPT?

More Ilia Anisa's questions See All

How do I perform a curve fitting if the model is in pde form with neumann boundary conditions?

if I have model in partial differential equation with Neumann boundary conditions, how can i do the curve-fitting with experimental data? I've planned to use optimization toolbox with lsqcurvefit...

11 December 2014 5,879 16 View

Can anybody help me regarding the mathematical study of plant extract?

why we need to use cumulative yield while plotting the graph of yield vs time instead of using non-cumulative? since for thermal labile compounds, the degradation (reducing of yield) observe for...

11 December 2014 2,778 6 View

Is there any difference for inputting the data of torsional energy if I use degree instead of radian?

I simulated my sample but I just recognized that I input the data in degree unit. Or do I need to change into radian and run again?

04 May 2014 345 2 View

How can pressure setting be adjusted in an MD simulation if in the real experimental work we ran at high pressure?

In one journal I read the real pressure was 25MPa, but in MD simulation, they applied 18.6MPa only. In my study, I used 10MPa but I don't know how to predict the pressure in MD simulation?...

03 April 2014 2,074 5 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

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

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

Tarak Karamakar

Same density!!

Did you keep box lengths same as in the final NPT .gro file?

I would rather suggest you to do the following

grompp -f nvt.mdp -c npt.gro -t npt.cpt -p system.top -o npt.tpr

then try to run the simulation.

I'm assuming that you have properly equilibrated (energy, volume, temperature) your system prior to this NVT run.

all the best.

Qiang Pei

This is unusual situation, I will suggest you to check the system relaxation, or the boundary situation, or if there is any structure conflict... You could check the output file of our initial NPT calculation or the input file of your NVT calculation, expecially the term related to momentum of each atom.