Science topics: Dynamical Simulations

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# Dynamical Simulations - Science topic

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Questions related to Dynamical Simulations

My position about Mach's Principle is that it is unsupported and refuted by optical and gravitational detection of Neutron Star Collisions.

I identified the only support (Celestial Dynamics within the Solar System requires instantaneous positions to be used in the force calculation) as being the result of using the wrong (empirical Newton's Law of Gravitation) law.

This shouldn't come up as a surprise to anyone since we all know that Newton's Law failed to predict the right Mercury Perihelion Precession Rate.

Of course, nobody can use Einstein's equations for a multi-planet dynamical simulation.

My theory - the Hypergeometrical Universe Theory (HU) provides a trivial replacement for Newtonian Dynamics and Einstein's General Relativity.

In fact, HU fully replaces General and Special Relativity.

**IN SUMMARY**

To call a theory Machian is a bad thing.

I need .gro, .itp, and .prm file for heteroatom for simulations of TM-proteins. Automated Topology Builder is not generating these files. Similar is the case with PRODRG? Any suggestions please.

Hello.

I am trying to use

**gromacs**to start an MD simulation of a protein-ligand complex.I was following the recommended tutorial http://www.mdtutorials.com/gmx/complex/index.html

- I did the system preparation, minimization and heating.

- I am trying to start an

**equilibrium**as a**continuation**from the**heating**, getting two errors: FATAL ERROR or INCONSISTENCY INPUT._____________________________________________________________________________

---> options in my

**step07_npt.mdp**file:[...]

continuation = yes ; continuing from NVT

[...]

gen_vel = no ; velocity generation off after NVT

_____________________________________________________________________________

running previous grompp to generate tpr.

_____________________________________________________________________________

**$ gmx_mpi grompp -f par/mdp/step07a_npt.mdp**

**-c str/complex/step06d_nvt_ann_LONG.gro**

**-r str/complex/step06d_nvt_ann_LONG.gro**

**-p top/top/test.top**

**-t bin/cpt/step06d_nvt_ann_LONG.cpt**

**-n str/idx/step06c_complex.ndx**

**-o bin/tpr/step07a_npt.tpr**

**-pp top/top/step07a_npt_POSRE.top**

**-po run/log/mdout/step07a_npt_mdout.mdp**

I tried different options:

[ step06_nvt is previous heating step - step07_npt is equilibrium step]

1. try running continuation from heating using heating output files:

_____________________________________________________________________________

**$ gmx_mpi mdrun -v -s bin/tpr/step07a_npt.tpr**

**-cpi bin/cpt/step06d_nvt_ann_LONG.cpt**

**-o bin/trj/step06d_nvt_ann_LONG.trr**

**-x bin/trj/step06d_nvt_ann_LONG.xtc**

**-cpo bin/cpt/step07a_npt.cpt -cpt 60**

**-c str/complex/step07a_npt.gro**

**-e bin/edr/step06d_nvt_ann_LONG.edr**

**-g run/log/mdlog/step06_nvt_ann_LONG.log**

ERROR:

>

**Inconsistency in user input:**

Some output files listed in the checkpoint file

bin/cpt/step06d_nvt_ann_LONG.cpt are not present or not named as the output

files by the current program:)

Expected output files that are present:

Expected output files that are not present or named differently:

run/log/mdlog/step06_nvt_ann_LONG.log

bin/trj/step06d_nvt_ann_LONG.xtc

bin/edr/step06d_nvt_ann_LONG.edr

To keep your simulation files safe, this simulation will not restart. Either

name your output files exactly the same as the previous simulation part (e.g.

with -deffnm or explicit naming), or make sure all the output files are

present (e.g. run from the same directory as the previous simulation part), or

instruct mdrun to write new output files with mdrun -noappend. In the last

case, you will not be able to use appending in future for this simulation.

_____________________________________________________________________________

2. running with noappend option and using new file names.

_____________________________________________________________________________

**$ gmx_mpi mdrun -v -s bin/tpr/step07a_npt.tpr**

**-cpi bin/cpt/step06d_nvt_ann_LONG.cpt**

**-o bin/trj/step07a_npt.trr**

**-x bin/trj/step07a_npt.xtc**

**-cpo bin/cpt/step07a_npt.cpt -cpt 60**

**-c str/complex/step07a_npt.gro**

**-e bin/edr/step07a_npt.edr**

**-g run/log/mdlog/step07a_npt.log**

**-noappend**

ERROR:

>

Fatal error:

**Cannot change a simulation algorithm**during a checkpoint restart. Perhaps you

should make a new .tpr with grompp -f new.mdp -t

bin/cpt/step06d_nvt_ann_LONG.cpt

_____________________________________________________________________________

I have a simulation code for a

**Horizontal Washing Machine.**The code solves the equations of motions of the system by

**Matlab ode45**and plots the**vibration response**of the system at the**transient state**of performance.In this code, the frequency (

**omega**) is an**exponential**function of time, as it's stated below (and its diagram is attached to 'the question'):-------------------------------------------------------------------------------------------------------------------------------------------------------

omega= (1-exp((-0.5)*t))*omega_0+(1-exp((-0.5)*heaviside(t-t1).*(t-t1)))*(omega_1-omega_0);

-------------------------------------------------------------------------------------------------------------------------------------------------------

**ode command:**

-----------------------------------------------------------------------------

[T,Y]=ode45(@snowa1,tspan1,initial_vector1);

plot(T,Y(:,1)-mean(Y(:,1)))

-----------------------------------------------------------------------------

**The resulting displacement response is attached to the question.**

**It is desired to**:

**First**, increase the frequency to omega_0 by exponential1

**Then**, increase it to omega_1 by exponential2

**But 'the problem' is**that:

the displacement response shows an

**unexpected increase in frequency**at the beginning of the second exponential increase (it**becomes 20 Hz,**which is much larger than the maximum frequency in the simulation- 10 Hz).Do you know what could be the reason for this response?

Any help would be gratefully appreciated.

Hi. I am running transmembrane protein simulation. I am confused at position restraining. During the shrinking steps using inflategro.pl script, tutorial mentions experimental value 0.69A but i do not experimental value in my case. Please help me about how many iterations I should perform?

quote from the book "Мathematical notes on the nature of the things"

-- So, conceptually, we proceed from the fact that the real Universe is a dynamic flow on a seven-dimensional sphere, therefore, a vacuum, without taking into account the evolutionary component, is a globally minimal vector field of matter accelerations, forming on the surface of the sphere $S^{7}$ a foliation $S^{1}\times S^{3}\times S^{3}$, a typical layer of which has the shape of a Clifford torus $S^{3}\times S^{3}$, and taking into account the periodicity of the foliation in time, its dynamics it is described by a toroidal manifold $S^{1}\times S^{1}\times S^{3}\times S^{3}$. However, since the globally minimal vector field of matter accelerations evolves to its absolutely minimal state so that in the process of evolution the radius of one of the spheres of the Clifford torus increases and the radius of the other sphere decreases, then there is no periodicity of foliation in time, and the dynamics of vacuum foliation is described by a cylindrical manifold $\mathbb{R}^{4}\times S^{1}\times S^{3}$ and it is convenient for the observer to operate with the space $M\times S^{1}\times S^ {3}$, where $M$ is Minkowski spacetime, and $S^{1}\times S^{3}$ is the compact component of the vacuum foliation.

Dynamic flows on a seven-dimensional sphere that do not coincide with the globally minimal vector field, but remain locally minimal vector fields of matter accelerations, we interpret as physical fields and particles. Moreover, bosons are associated with point-like perturbations of the vacuum vector field, and fermions are associated with node-like perturbations of the vacuum vector field, that is, the current lines of fermionic vector fields have a topological feature in the form of nodes. -- (p. 16)

(19) (PDF) MATHEMATICAL NOTES ON THE NATURE OF THINGS (researchgate.net)

I want to import 3D field data of an accelerating structure designed in CST to ASTRA for beam dynamics simulations. I written a matlab script to do that and try to qualify the same with an

azimuthally symmetric structure. When I compared the results of ASTRA for (1) cavity field given as Z, Ez and (2) cavity field given a 3D fields . I observed that Energy gain is same for both the cases but other beam parameters viz. beam size, emittance are very different. I compared the cavity field plots (both Ez vs Z and Ex/x,Ey/y vs z) in both the cases and they are same. Does anyone can help by proving a tested matlab script to convert the CST field data to ASTRA input format and any experience/observation of comparison of ASTRA results with and without 3D fields.

If so, how do you calculate refrigerant properties?

The delayed dynamical system is as follows:

dx/dt= -Betta*x(t)+F(x(t))+(Betta-1)F(x(t-d)),

x(t)=Phi(t) for t in[-d, 0] where d is delay and F(x(t)) is a projection function. I have Matlab code (using ODE45) for this delayed dynamical system without delay, but when the delayed added I don't know how I can insert the delay.

I would be very grateful if someone could help me to design Matlab code for such delayed dynamical system?

i am a bio technologist and i am initiating the molecular dynamics and mathematical and computational modelling of silver nanoparticles synthesis and their interaction with blood stream. and i am unable to find a starting point for this project. any sort of help would be highly appreciated. and we can collaborate for this particular project as well.

hoping to get a rapid response.

I am in need of Mathematical model of MRE to study its dynamic behavior under varying magnetic field to design MRE based Dynamic vibration absorber