Science topics: Dynamical Simulations
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# Dynamical Simulations - Science topic

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Question
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.
Mach's principle, or, as I like to call it "Mocks principle" is essentially a refutation of Newton's second Law. It is positively one of the most idiotic ideas in physics, but because it is always expressed by respected scientists in awed tones nobody notices.
Newton's second states, essentially, that acceleration is equal to the net force on an object divided by its mass.
What mocks principle does is says, no... we're not going to do that. We're going to say that
amach = a-mg = ∑Fng/m
Where Fng is the net non-gravitational force acting on the particle,
But then on top of that, we're going to add a whole bunch of other complete claptrap, to wow and amaze people, so it seems like we've just done something clever in conflating real and fictitious forces.
It's also one of those "Emperor's New Clothes" sorts of things, so if you point to the fact that you've spent a considerable amount of time in College Freshman physics making a distinction between real and fictitious forces, people in the general relativity community will cluck and guffaw about how foolish and uneducated you are to fail to conflate them, once Mach's principle is introduced.
Question
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.
You can try with Charmm GUI to generate prm file using ligand reader and modeler, ATB does not provide prm file.
Question
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.
_____________________________________________________________________________
$gmx_mpi mdrun -v -s bin/tpr/step07a_npt.tpr -cpi bin/cpt/step06d_nvt_ann_LONG.cpt -o bin/trj/step07a_npt.trr -x bin/trj/step07a_npt.xtc -cpo bin/cpt/step07a_npt.cpt -cpt 60 -c str/complex/step07a_npt.gro -e bin/edr/step07a_npt.edr -g run/log/mdlog/step07a_npt.log -noappend ERROR: > Fatal error: Cannot change a simulation algorithm during a checkpoint restart. Perhaps you should make a new .tpr with grompp -f new.mdp -t bin/cpt/step06d_nvt_ann_LONG.cpt _____________________________________________________________________________ Relevant answer My understanding is that you produced a new binary (step07a_npt.tpr) from a new .mdp file (step07a_npt.mdp), and now you are trying to continue the previous nvt run (step06d_nvt.*0, right? In that case this is wrong$ 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
You are using a NEW mdp file, and generated a NEW binary. The info from the previous state should be already inside the new binary, that's why in the preprocessor phase you wrote the flags -c, -r, and -t. Therefore this
$gmx_mpi mdrun -v -s bin/tpr/step07a_npt.tpr should do the work. Consider that -o, -x etc specify the OUTPUT options, not the input, therefore when you write -x bin/trj/step06d_nvt_ann_LONG.xtc you are telling mdrun to write your trajectory to that file, not to take from that file and continue it. The error you get in the first case is related to the fact that the -cpi option is a continuation from a checkpoint, which is going to search for some files to continue a given run. This is useful when a simulation crashes or when you want to make a simulation longer. For example, you run 100ns of something and would like to go to 150ns. Then you run gmx conver-tpr, you extend the tpr file time and continue from there (using -cpi flag, read https://manual.gromacs.org/documentation/current/user-guide/managing-simulations.html) Here you got a new tpr, so you don't have to specify the -cpi flag. Second error is similar. You are going from NVT to NpT, therefore you are now coupling the pressure. What mdrun is telling you is that it is not able to go on with the NVT phase because the tpr you are using (the step07) has something different from the state you are trying to continue (step06), most likely the barostat but something else as well for sure. If you want to make the NVT longer you can go gmx convert-tpr -s npt.tpr -extend TIME_YOU_WANT_TO_EXTEND_IN_PS and then go gmx mdrun -v -s npt.tpr -cpi npt.cpt In this case you want a NpT, so a change in the binary, therefore you (rightly) compiled a new tpr (specifying the input status with -c/-r/-t flags) and can now just run the gmx mdrun -v -s npt.tpr Hope this is clear! :) Nicola Question 13 answers 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. Relevant answer I understand that the 4DOF system for the washer can be quite lengthy. However, I'm unsure if your question is a control problem. If it is, and the 4DOF mathematical model can be expressed in such form: x' = f(x) + g(xFc(ω) where 1. f(x) = [f1(x), f2(x), f3(x), f4(x)]T and g(x) are the nonlinear terms in column vector forms that you derived from the Lagrangian method, 2. Fc(ω) is the control force that represents a function of ω in vector form, and 3. ω (omega) is the control input, then I think it is possible to design the spin speed profile for the control input, ω, so that the desired responses of x can be achieved. If you want to design the profile, you need to at least understand the mathematical equation for Fc(ω). Do you want to regulate the spin speed at 300 rpm, 600 rpm, or 1200 rpm? Because I see only the signal oscillates within the dimensionless amplitudes ± 4×10–3. I have plotted the signal according to your suggestion, and compared it with Mahdi's original signal. Note that if t1 > 5/τ, then exp(–τ·θ(t – t1)·t) ≈ 0 after t1, because exp(–0.5·t) has decayed to almost zero. Question 5 answers 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? Relevant answer Any questions can contact Zeeshan Zafar Question 10 answers 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)
About the dynamics of features
In our collapsed Finsler metric space, let the trajectories of the vector field features be helical lines, and therefore the features themselves make their own angle of rotation, and thus they have such a characteristic as angular velocity. Note also that the trajectories described by perturbations of the vector field have a regular helical shape only in vacuum, that is, in the absence of fields (distortions of the globally minimal vector field), while gravitational fields change the pitch of the helical lines, and calibration fields are responsible for twisting the helical lines.
Question
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.
Dear Chaipattana Saisaard and Y. Chen ,
Thanks for useful suggestions. I will try these and get back to you.
Shankar
Question
If so, how do you calculate refrigerant properties?
you can try coolprop: http://www.coolprop.org/ they have a Modelica interface
Question
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?
Dear Israel Tankam,
Thank you very much for your complete and valuable answer. I will use it.
Kind regards,
Question
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.
Hello Mr. Hashmi
The key element of your study is "Hemocompatibility".
You must make sure that:
1 - Clotting time of normal plasma will not be affected by the particles.
2 - Platelet function (activation and aggregation upon proper stimuli) will not be affected by the particles
3 - Red blood cells and Leucocytes will not be harmed (e.g hemolysis or cell toxicity) by the polymer or its fragments.
From the in silico point of view, you can always evaluate how fragments of your polymer will interact with clotting factors and different phospholipid membranes (resambling platelets, RBC and WBC)... Picking up key elements of the coagulation cascade such as thrombin should be a good start for docking and molecular dynamics analysis. Same goes as a simple bilayer model with phosphatidylcholine and cholesterol.
Optimal settings for your environment would be:
pH 7.4
37 Celsius
And a high ionic-strength media (See Tyrode Buffer composition for ions)
If you want to keep the environment as simple as possible for computational memory/time sake, just make sure you will have sodium chloride, calcium chloride phosphate and carbonate (see PBS composition, I've added carbonate due to its importance as a buffer).
Wish you best of luck in your project.
Andre
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