Topology - Science topic

There are several known contributions of Topology to ML.

But: what has been the contributions of ML to the research on General Topology, and particularly to Finite Topological Spaces? Do you have any information of this regard?

I am working on molecular docking and dynamic simulation of protein-ligand complex, and the complex generated MD.xtc file of 4.3 gb which I am unable to open in UCSF Chimera through MD movie option. I know that limited RAM of my system is creating this issue, but is there any other way to do it.

I also found that spliting trajectory file helps, but I am getting the following error (Screenshot 2023-11-27 13-31-13.png) while entering MD.tpr and MD.xtc in MD movie Gromacs option. Which I know is because the topology file is not splited like the trajectory file. So, how to rectify this issue, if there's no other way to work around.?

I am using Ubuntu OS, with 8gb ram, 2gb graphics 1650.

Q=1: How can plot 3D graphs for topological indices by using Mathematica software??

Request:

Plz send any coding for 3D mash graph related to attached sample graphs.

I would like to perform a shape optimization on a topology optimized component without exporting and importing the part as .stl, since in that way I loose all the properties, the loads and the BC. Please, is there any chance to to this?

The main website is broken and I can't find the topology dataset I want for my experiment.

I've been wondering because the definition of an eta-open set is if A ⊆ int(cl(int(A))) U cl(int(A)). While the semi-open set is if A ⊆ cl(int(A)). So, if int(cl(int(A))) just a subset of cl(int(A)), then int(cl(int(A))) U cl(int(A)) = cl(int(A)). This implies that an eta-open set is equivalent to a semi-open set. Can anyone enlighten me with this? because I've looking for examples that make these two sets not equivalent and still nothing found yet.

Maybe in general (on metric spaces, etc).

F(X,Y)= set of all functions from a topological space X to other space Y.

C(X,Y)= set of all continuous functions from a topological space X to other space Y

Compact open and compact convergence topology are comparable, if Yes then which one is finer on F(X,Y) (not on C(X,Y))

Will it be a Majorana mode? But, Majorana modes are typically characterized by their strong localization at one end. If an edge mode is not strongly localized at one end and extends significantly along the other edge, could be an ordinary edge state or a different type of topological mode?

I am working on topology optimization using the parametric level set method. Regardless of the methodology, I thought it might be a generic problem in Topology optimization with which many researchers in the field have faced. The problem is that I cannot achieve smooth boundaries even though I am using the level-set method to produce smooth boundaries. I am using two different grids and meshes for the mechanical and the level-set domains. I thought I needed to increase the number of Finite elements from 350 to 1000, but nothing changed, you can see it from the bottom right figure. Nor did increasing the number of grid cells in the level set domain improve my result.

Thank you in advance for your help.

Best regards,

Farzad

In spite of such effects, the majority of humanity, especially the scientific community – does not learn to bring about a radical re-definition of the pragmatically defined concept of attainable truth. This is the proof of the relevance of a re-formulation of the same by the science of philosophy and by scientific philosophy in the realization and growth of science, technology, etc.

Just within the pragmatic attitude lives and functions a big majority of the humanity. Specifically, the scientific community acts consciously by inhibiting wholesome ideas, actions, and changes in the usually pragmatic functioning of (1) every possible realm of knowledge, including the human project of thinking, feeling, curing, facilitating, etc. or (2) any other realms of life in any given environment and society.

The only given justification has been the urgency (1) to experience “the realizably” theoretical and practical effects of all ideas, actions, and changes as early as possible, (2) to have the awaited “long-term effects” at the earliest, (3) to have it in abundance “in the here-and-now”, etc.

Pragmatism has been the backbone of almost all, most basic and less basic, definitions, practical procedures, etc. in logic, mathematics, physical sciences, biological sciences, human sciences, etc. Pragmatism acquires constantly new definitions in history of science and philosophy.

By ‘pragmatism’ is meant not exactly and not only the philosophical school under this name. Of course, this philosophical school extols the effects-only and use-only theory beyond the emphasis it assigns to theoretical breadths and depths. In general, such emphasis plays an exaggerated role in determining the forms of access to what humanity needs in terms of life and truth. It is mainly the sciences that effectively inhibit any efforts beyond pragmatism.

The suggested new paradigm beyond pragmatism would be: The more the certainty and generality of the theoretical breadths and depths assured by the axiomatic foundations – the greater the truth of the specific, the individual, and the delineated results of such a founded philosophy and science within life and knowing.

I shall explain in other words the pragmatic state of the sciences. After all theoretical and experimental search, truth is being concluded to – albeit for a short time and with some or much assurance of probabilistic tenability – in a manner that is FULLY representative of the state of affairs sought to be represented.

The representation of an objectual process in a truth statement is taken to directly correspond or correspond enough to reality, when the theoretically antecedent instruments are universal enough to produce the knowledge about anything specific. But the antecedents are never universal enough, if the theoretical foundations are not broader than the theoretical grounding available in the positive sciences or formal sciences.

This sort of truth-representation is what knows, feels, cures, and facilitates life today, purportedly “in all respects”. Hence, pragmatism is merely be about the method of approaching truths and activities. But it has not been sufficiently about concluding something from a swarm of structures of theoretical generality and superiority, which should have worked in terms of theoretical and practical applicability in all possible specific cases available in any theory that is trans-pragmatic.

One example where the attitude of more general theoretical justification is missing is in the diverse theoretical constructs in physics. Anyone can characterise one of the many reasons as the blind and pragmatic acceptance, by many physicists, of the velocity of light as sacrosanct everywhere in the cosmos. In fact, we have been able to prove the velocity of light only with respect to our part of the universe, and have accepted it as the highest for all parts of the cosmos solely because we have not been able to detect one of higher value.

This is due to the overemphasis on pragmatism in science. Using such a limit velocity in science for technological success is a necessity, but insisting on it even in the broadest possible theoretical situations is cheap adherence. In this respect, the matter that none can accept is the way in which Einstein’s postulation of c as the reference velocity to measure and calculate other but lower velocities becomes accepted as the final proof of the very postulation!

What else is it but the consequence of strict pragmatism in the method and procedure of inquiry without enough antecedent theoretical broadening in the foundations, method, and procedure? This has debilitated science and philosophy of science for almost a century and a quarter. How to dispense with such pragmatism in science and philosophy?

Additionally, the declaration that the observed source-independence of luminal velocity is somehow a basis for accepting a background ether for luminal velocity to hinge upon, is again another instance of overmuch pragmatism in the method and procedure of theorization without restricting strict pragmatism to drawing conclusions.

A second example of strict pragmatism is the way in which some absolutely spherical geometries and their topologies were and are even now being used to geometrize the universe. They tend even to conclude from such a presupposition that the universe is spatially and temporally isotropic, and then tend to dispense with the effects of the locally causal temporal dimension on the universe.

Yet another example is the blind acceptance of the pragmatically probabilistic interpretation of quantum physics as the essence of all physics and of all physically existent reality, whereby most physicists attempt to accept a merely epistemic sort of causality in physical reality and call it “probabilistic causality”, and then start using it as if it were physical-ontological causality.

What we can understand (probabilistically, epistemically) need not be the same as how nature is out there! What in fact is the probabilistic causality that acts in physical processes with some parts of it being causal and other parts not causal or even acausal? Is not such a concept of causality a silly idea of causation based on epistemic determinism getting converted into ontological determinism, which then is converted into the actual nature of existent processes? The unnecessarily pragmatic ways of fixing scientific practices is the main reason behind it.

In preparing a short introduction to the following critical presentation of the aftermaths of pragmatism, let me put in gist the new paradigm that is necessitated here: (1) Truth is not merely a subject-object act. (2) Truth is not merely an act of tending towards. (3) Truth is much more an act of epochal finalizing of constant insertion of foundational breadths and depths in the state of affair / process being inquired into, based on the most universal of all conceptual foundations and driving them down onto the particular, but based fully and always on the foundations of the total in a mutually related context.

That is, strict pragmatism should be exercised only at the instance of concluding to the final, strictly contextual, statement and action, and that too under the provision of further constant inquiry and enhancement of the descriptions, conclusions, etc.

My contention concerning strict methodological pragmatism is that, although the pragmatic attitude has its rights over thought and practice, it (1) inevitably foregoes many fundamental (most broadly based on the totality of all existents) aspects of reality, environment, and life and, (2) in consequence, unbridles back onto the same reality, environment, and life the epistemically guided ontological aftermaths of the negligence of the said fundamental theoretical aspects and necessities of reality and of knowledge – and consequently of course onto life and the human ideal of comprehension of reality and life.

Hence, it is high time that philosophy and science eliminate as much as possible the defective, strictly pragmatic attitude from their foundations while safeguarding some of the necessary aspects of pragmatism merely when they create advantages via accessing conclusions and actions, without causing philosophical, scientific, and human-life tragedies.

As there are countless disadvantageous aftermaths of pragmatism in knowledge and life, some of them may be cited in the following:

(1) International, national, and local politics purposefully manipulating natural resources, economies, societies, religions, and nations for power and wealth, even to the extent of impoverishing the majority of a continent or nation.

(2) National and international poverty alleviation programs and techniques which increase the rich-to-poor differences by perpetuating pragmatically charitable corruption in industrial, educational, health, and governmental ventures.

(3) Educational systems and methods becoming partially aimed at creating a vast majority of cheap labourers for the industry especially in poor nations, by fast-paced and obscurantist information-encrypting of sciences, humanities, and languages in educational institutions, without reference to the history of future-oriented achievements in discoveries, ideas, theories, events, programs, etc.

(4) Most media entities creating sensational partial truths as the short-time highest truths at the behest of politicians, industry, research & development, or at least against them, meant finally for easy financial gains and thereafter for practising political and scientific amnesia at the same truths.

(5) The pharma and health industry adopting and justifying as sacrosanct the mechanist-causalist manners of producing medicaments and treating patients – encouraged mainly by the successes of naturally necessitated urgency in such interventions – and producing chemical medicines so non-holistically (i.e., in ways that do not involve material interactions more minute and life-based than in chemical interactions) that the methods of production and treatment necessarily have more than intended side-effects creating ever more patients.

(6) Industries, technological companies, media entities, media producers, and a few nations specializing in hyperbolically creating and satisfying unhealthy and unessential psychological and physical needs and increasing easy production of commodities for quick-growth in economy, resulting in universal pollution of genes and life-forms.

(7) Constitutions of nations and justice-dispensation systems formulated in ways that normally foster or at least merely facilitate the exigencies of the powerful and rich and possibly get favoured in return.

(8) Governmental law-enforcement arms which work on old-fashioned and corruption-facilitating machinery and, from time to time, can milk the rich and powerful by way of protection of their pragmatic socio-economic attitudes.

(9) The more than two centuries of spread of chemical fertilizing methods of agriculture by blocking the spread of great natural cultivation methods and researches into them, callously titling the latter “unscientific”, and thereby chemically cluttering the whole cultivable and life-worthy earth.

(10) The millennia-old mammoth culinary science and eating culture that encourage tasty junk consumption at home and outside, successfully encouraging and perpetuating the enjoyment of quick pleasure from the one end of the tongue to the other.

(11) The way in which human beings, for millennia, exhaust and emaciate themselves in pursuit of quick joys, vastly unaware of the merely brain-based connotative nature of quick joys.

(12) The methods of finance acquisition and offspring-maintenance in families, societies, nations, and religions, oriented at self-perpetuation and attaining – for that same reason – nothing of it.

(13) Eco-compatibility efforts all over the nations by governments themselves, that help further industrialize under cover of grand holistic statements and schemes.

(14) Economic, educational, cultural, health, and other diverse forms of solution of problems of humanity, in which policy makers never go for the deepest roots of maladies: e.g., the real reason why people build houses on and cultivate (e.g., occupying and cultivating steep hill-sides, thus inundating the high ranges), is not merely craving, but the high rate of population growth, and yet no government acts in this direction ethically and democratically via education.

(15) The manner in which the very oppressed groups become much like the oppressor groups and indulge in pragmatic tactics against their own status, and consume the effects of such self-poisoning.

(16) The universal ignominy to what the experiences and the universal phenomenon of rational reflections of the old and dying are – including those of former scientists, technocrats, and scholars.

(17) The wide-spread technocratic and allopathic health-scientific methods of nipping all nature-infused living methods by blanket-terming them as unscientific.

(18) Religions’ millennia-old and continuing promise of a quick and miraculous transfer to a body-less state similar to that of a supposedly vacuous Absolute, instead of the more possible and reasonable “continued growth” of love-bodies as fully well caused by the same kind of growth during the lifetime of individuals and societies in imitation of an infinitely active love-bodied Source.

(19) A section of scientists and philosophers wilfully presupposing that anthropomorphized expressions and theologies based on them are the meaning of religion and spirituality, and basing their science, technology, medicine, and philosophy, etc. on notions that counteract these vicious concepts that should not have been the meaning of religion and spirituality.

(20) Some or many of those involved pragmatically in the above thought patterns and sciences trade their guns against supposed realities that do not exist in the sciences and in the world out there, thus beating in the air to kill some form of ideas that do not exist where they think them to exist.

The most suitable examples today in theoretical sciences are Russell, Wittgenstein, and many others in the early half of the 20thcentury, and Stephen Hawking, Richard Dawkins, Lawrence Krauss, and a host of others in the latter half of the 20th century and thereafter. The ways in which the likes of these experts have unquestioningly been using the already existing pragmatism in physics, cosmology, and philosophy is symbolic and emblematic of pragmatism as a cut-throat methodology in effect.

Technological examples are the ways in which Newton’s physics and mechanistic chemistry, biology, economics, etc. are being used today to facilitate money-flow into the industry by disregarding their health-related and environmental aftermaths.

Bibliography

(1) Gravitational Coalescence Paradox and Cosmogenetic Causality in Quantum Astrophysical Cosmology, 647 pp., Berlin, 2018.

(2) Physics without Metaphysics? Categories of Second Generation Scientific Ontology, 386 pp., Frankfurt, 2015.

(3) Causal Ubiquity in Quantum Physics: A Superluminal and Local-Causal Physical Ontology, 361 pp., Frankfurt, 2014.

(4) Essential Cosmology and Philosophy for All: Gravitational Coalescence Cosmology, 92 pp., KDP Amazon, 2022, 2nd Edition.

(5) Essenzielle Kosmologie und Philosophie für alle: Gravitational-Koaleszenz-Kosmologie, 104 pp., KDP Amazon, 2022, 1st Edition.

Are its faces polytopes?

Is there any information in the literature on the geometry and topology of saddle polyhedra?

Can we use them to construct structural triply periodic minimal surfaces?

An attempt to answer some of these questions in:

Are the oil-water partition efficient (logP) and Topological polar surface area (TPSA) of energetic compounds related to their molecular stability? How do these parameters relate to the molecular structure?

Generally, a topology tau on a set X is defined considering the following three axioms:

1. The whole set X and empty sets are in topology tau.

2. Arbitrary union of any collection of open sets of tau is in tau.

3. Finite intersection of any collection of open sets of tau is in tau.

Is it possible to construct a topology tau on X without considering first axiom?

To study the topology of the MOF crystals

I am writing to seek assistance on a matter related to n2t file generation. I am using GROMACS and charmm36 force field in my work. I am covalently attaching a short polymer(poly-peptide) to a nanosheet with the carbonyl carbon of the polymer attached to the nitrogen of the nanosheet I obtained the parameter(itp file) for the polypeptide from CGENFF then added the corresponding atom types and charges from the itp to my n2t file the monomer of the poly-peptide is histidine and it’s itp file has various hydrogen atom type along with carbon types with different charges I have added them all in the n2t file in the same sequence as in the itp since most these atom types are attached to carbon when topology is created using x2top wrong type of carbon and consequently wrong charge is assigned to the atom of my structure. I want you to note the hydrogen types as well as the nitrogen type NG2R51 in the topology file at line 134 it is supposed to be a NG2S1 nitrogen type with a -0.555 charge. There are many other atoms whose atom type was supposed to be different. How can I obtain correct topology.I am attaching the itp file(plh.itp) along with the ss of topology and n2t file. Any guidance or pointers would be of immense help. Thank you for your time.

Are there any publications on the topological properties of nonstoichiometry loci - in general and, in particular, in intermetallic compounds?

Let (X, tau, I) be an ideal topology I ask:

wThe product of this topology itself is ideal topology or not?

Hi.

I am trying to create ligand topology and parameter files using SwissParam webserver. I followed all the steps to create the .mol2 file available in SwissParam page: https://www.swissparam.ch/SwissParam_mol2_file.html.

But this error keeps on coming:

Unfortunately, topology and parameters were not successfully generated for LIG.mol2. A failure report can be found below. Failure report: Possible problem with molecular topology in LIG.mol2. SwissParam will try to reconstruct the topology from coordinates only. Topology and parameters were NOT generated. Please check the validity of your molecule. - Are all hydrogens present in the mol2 file? - Is the mol2 file correct? Please, read "How to obtain a correct mol2 file?" in the www.swissparam.ch website.

For reference, I am providing my ligand.mol2 file and lig_fix.mol2 which I have created for performing protein-ligand simulation using Gromacs and CHarmm27 forcefield.

Please help me solve this query.

Thank you for consideration.

Alvea Tasneem

I have been using PRODRG for small molecules topology for years, but now I can't access it, I have emailed its developers but couldn't get any response. I want to use Gromacs forcefield, so I have only 2 options, one is ATB which is not free for new molecules, and another one was PRODRG. Kindly give me suggestions if you know any other way. I have tried Swissparam and switched to Charmm ff but it also didn't work and gave me errors with LJ and at the energy minimization step.

I am starting a new area of research that is Algebraic topology. Kindly suggest some latest problems and related publications

I am having an issue regarding Phosphatidic acid topology generation for Gromacs 5.1.5 simulation. I would like to study the protein-ligand dynamics. Kindly help

After running this step to create ligand topology for molecular dynamic simulation protein-ligand complex:

It showed some tracebacks and import error:

I tried to generate charmm36 topology and parameter files for copper ions on laccase enzyme but it presents an error that says "No residue in CHARMM forcefield". So I've tried CSML Search to parameterize ligand FF using PDB coordinates but the erros persists.

I am new to amber any trying to use xleap to make a tetrapeptide tuftsin. After solvation with TIP3PBox 14.0 iso, when I try to save the inpcrd and prmtop file using command

saveamberparm foo tuftsin.inpcrd tuftsin.prmtop

it gives following message

Checking Unit.

WARNING: There is a bond of 3.610664 angstroms between:

------- .R<WAT 886>.A<H1 2> and .R<WAT 886>.A<O 1>

WARNING: There is a bond of 4.162462 angstroms between:

------- .R<WAT 886>.A<H2 3> and .R<WAT 886>.A<H1 2>

WARNING: The unperturbed charge of the unit: 2.000000 is not zero.

-- ignoring the warnings.

Building topology.

Building atom parameters.

Building bond parameters.

Building angle parameters.

Building proper torsion parameters.

Building improper torsion parameters.

total 11 improper torsions applied

Building H-Bond parameters.

Incorporating Non-Bonded adjustments.

Not Marking per-residue atom chain types.

Marking per-residue atom chain types.

(Residues lacking connect0/connect1 -

these don't have chain types marked:

res total affected

CARG 1

I am not getting how to solve this error message.

I want to simulate a grid-road topology (organized streets) with vehicles generate traffic to Road Side Unit (RSUs). Also, if I need to ramp up quickly to 100 or 200 vehicles how can I do that?

12

If we want to calculate several M-polynomials which method is the most suitable.

I ran gromacs with command: grompp -f ions.mdp -c protein a_solv.gro -p topol.top -o ions.tpr. and yielded a Fatal error:

number of coordinates in coordinate file (solv.gro, 57741)

does not match topology (topol.top, 57742)

how to correct the match of protein a.gro and topol.top file?

While I was trying to generate ligand topology using CGENFF, the penalty score exceeded 50 (parameter penalty 141; charge penalty= 56.475). how do I reparameterize to obtain acceptable penalty score range?

It seems that the most simple way to get both an infinite number of tessellated solids and lattices with periodic minimal surfaces in R3 consists on using a Pearce "saddle tetrahedron". The resultant convex solids:

1) Have configurations which tesselate the euclidean space. These tesselations are not Voronoi and have curved boundaries in a bcc lattice.

2) Define minimal surfaces for any 3 dimensional quadrelateral on the external closed surface of the solid.

Is there any topological description of such solids in the literature? How can we get a Weierstrass representation of the external surface of each polyhedron? How can we get the conjugate continous surfaces? Can we consider this to be a good design method for structural lattices?

Any comment will be wellcome.

The fixed point property is a fundamental concept in topology and has been extensively studied in various contexts. However, there are still several open problems related to the fixed point property. There are many other interesting questions and directions of research in this area.

I am trying to find out the topological hall effect for my system of study. I currently have no idea about the process and what software packages to use. I know that we can find the anomalous hall effect (AHE) using the Wannier90 package. Any suggestions regarding this will be greatly appreciated.

I want to perform MD simulation on a protein that contains water molecules in PDB what forcefield parameters (topology/ parameter ) files should one use ?

Hello everyone,

While performing MD simulations of protein - ligand complex, at the adding ions stage I am facing an error :

Fatal error:

Syntax error - File UNK_fix.itp, line 7

Last line read:

'[ atomtypes ] '

Invalid order for directive atomtypes

Well, since I've used Swissparam to write the topology file of the ligand (UNK_fix.gro) which usually uses CHARMM all atom forcefield and the protein topology I've written with the charmm36-2019.ff. Can this be a reason that I'm facing the above error?

I've also referred to other options like #include statements which I suppose are correct and the editing in topology is all done right. For reference:

; Include Position restraint file

#ifdef POSRES

#include "posre.itp"

#endif

; Include ligand topology

#include "UNK_fix.itp"

; Include water topology

#include "./charmm36-mar2019.ff/tip3p.itp"

#ifdef POSRES_WATER

; Position restraint for each water oxygen

[ position_restraints ]

; i funct fcx fcy fcz

1 1 1000 1000 1000

#endif

; Include topology for ions

#include "./charmm36-mar2019.ff/ions.itp"

[ system ]

; Name

Protein in water

[ molecules ]

; Compound #mols

Protein 1

UNK 1

SOL 24553

So, please guide me through any other suggestions which may correct this error.

Thank you in advance!

Hi all,

Please suggest how I need to optimize a small molecule to generate the topology file for the ligand to process it for Protein-Ligand MD simulations.

I have tried to balance the valency of the molecule, after which I have submitted the molecule to CGenff server, but the charge penalty and penalty scores were very high.

After which I have tried to optimize the molecule using Avogadro software. Using the output from Avogadro, I have resubmitted the molecule to CGenff server, after which the penalty score was even higher.

I have also tried PRODRG and ATB but the molecule was broken in case of PRODRG, while processing for MD. The molecule contains 1 chlorine atom, also attaching the warning suggested by ATB server.

Kindly suggest how can I process this molecule? I am really new to this work. Please suggest if I am processing it appropriately or not.

I want to use cpptraj for some analysis but I need to convert my topology and trajectory files from Gromacs xtc, tpr format to Amber nc and parm formats. Could you please let me know how can I convert topology and trajectory files from Gromacs to Amber?

How to prepare topology file for coordination (complex) compounds. Topology files for organic ligand molecules can be obtained using online servers such as SwissParam and etc. How to prepare a topology file for a metal-containing ligand?

gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

Fatal error: number of coordinates in coordinate file (solv.gro, 198459)             does not match topology (topol.top, 198458)

Hi everyone,

I'm trying to optimize a very simple steel element (see figure) with a cyclic load applied in the two red regions. The settings are the standard ones (minimize strain energy, final volume 30%) However, after 6 cycles, the optimization process plot shows a flat curve and the result confirms that something has gone wrong. How can I solve the problem?

many thanks in advance

In fact, the phase will affect the amplitude distribution. For example, the OAM phase will cause the amplitude center to produce a small circle with an intensity of 0, and it will become larger as the topological value of the phase increases.

A physics experiment [1], driven on an expanding spin-orbit coupled Bose-Einstein condensate, suggested that a self-trapping effect band (explained in terms of the Peierls-Nabarro energy barrier) separates two dispersion domains characterized by a positive mass but a spin reversal. The self-trapping phenomenon was naturally explained by a negative effective mass related to a negative curvature of the underlying dispersion relation (as opposed to parabolic curvatures).

To better contextualise my question from a practical point of view, I will quote Wikipedia ( follow https://en.wikipedia.org/wiki/Spin_(physics) ): “Mathematically, quantum-mechanical spin states are described by ‘vector-like objects’ known as spinors. There are subtle differences between the behavior of spinors and vectors under coordinate rotations. For example, rotating a spin-1/2 particle by 360° does not bring it back to the same quantum state, but to the state with the opposite quantum phase; this is detectable, in principle, with interference experiments. To return the particle to its exact original state, one needs a 720° rotation (The Plate trick and Möbius strip give non-quantum analogies).”

I appeal here to physicists in a spirit of free and friendly discussion.

Hi everyone,

I work on Abaqus for a project and I want to optmise a part (topoogy + shape). I created the model an ran the topology optimisation. Now I want to extract the result geometry to make some shape optimisation. Is it possible to make it directly from Abaqus or with a Pyhton script or do I need to convert it in a CAD software ?

Thank for your help

I'm having trouble doing network analysis due to topological errors. I am using ArcGis software.

WARNING: topology has 41102 atoms, whereas trajectory has 3597

If a string vibrates at 256 cycles per seconds then counting 256 cycles is the measure of 1 second. The number is real because it measures time and the number is arbitrary because it does not have to be 1 second that is used.

This establishes that the pitch is a point with the real number topology, right?

I just read the article in "Australian Science Illustrated" about supersonic planes breaking the sound barrier and it gave me a very interesting thought that's related to an article I had published in a science journal last month. My article's called

"Riemann hypothesis supports topological propulsion and faster-than-light travel through space-time"

(10) (PDF) Riemann Hypothesis Supports Topological Propulsion and Faster-than-light Travel Through Space-time (researchgate.net)

and it was inspired by another article in "Cosmos" magazine (I started subscribing to Cosmos at the same time I subscribed to Science Illustrated).

SI's piece about the sound barrier says, "Sound waves in front of the plane become so compressed that they join together to form a shock wave."

My interesting thought is, "My paper builds on a 1919 paper by Einstein called "Do gravitational fields play an essential role in the structure of elementary particles?" Matter associated with the UFO becomes so compressed that the 3rd dimension can vanish from the parallelogram describing how gravitational and electromagnetic waves produce mass (Figure 2). This causes the top and bottom of the parallelogram to join together and form friction between the opposing movements of gravitation's gravitons and electromagnetism's photons. Their interaction is described using General Relativity's refraction of starlight passing the Sun and biology's "lock and key" mechanism where chemicals attach to receptors of the correct shape. Joining of the parallelogram's top and bottom also creates the single surface of the Mobius strip which my article says is a fundamental building block of space-time and everything in the universe."

This presents two equally valid ways of viewing space-time, The first is to conclude that space-time is curved since the curvature inherent in Mobius strips (plus figure-8 Klein bottles and Wick rotation) determines the shape of space-time. The second is to assume space-time is flat (uncurved ... though containing curves) since, as the journal article states, "gravity may deflect light because the latter’s photons are a key fitting into the former’s graviton-locks. This makes sense if trillions of Mobius strips make up a photon, and trillions of figure-8 Klein bottles make a graviton. Photons and gravitons fit together because Mobius strips and figure-8 Klein bottles fit together – as noted above, the second topological shape is called a Mobius Doublet since it’s a joining of two strips."

from OPLS all-atom force field we can make simply using x2top command.

Hello everyone.

Please help me to understand this agarose gel. I did a plasmid (Pgem vector with an insert with an expected size of about 3kb, from E.coli) extraction with a simple protocol Birnboim e Doly (1979). The first two bands are the different topologies of the plasmid. What I need to know is the last band (very intense) - It's very small and lower than 100bp (maker is 100bp plus). What could it be? Thanks

Standard tuning for guitar E A D G B E comes around frequently but the old lute tuning E A D G C F is rarely if ever used.

Looking at the gradients, standard tuning is 0 5 5 5 4 5 and the lute tuning is 0 5 5 5 5 5, so the strings in standard span two octaves 0 5 10 15 19 24, while the lute tuning 0 5 10 15 20 25 has one more note than standard.

Same number of points, different number of notes. That makes two different topologies, so we have a collection of guitar topologies that make a theory of guitar.

When guitar strings have one note in common, they have every note in common. Then the guitars have the same set of pitch values (since they can form a union in which every note sounds in tune) but two guitars may have a different number of notes. The notes may be located at different points on guitar.

The number of notes and the number of frets on the guitar is not critical to structure because the structure is basically the same the same with a few more or less but changing the tuning by just one note is critical because it completely changes utility of the structure.

So 0 5 5 5 4 5 is a very, very good number but 0 5 5 5 5 5 is bad number.

It is clear the lute tuning is not as rich as standard because the regularity of 0 5 5 5 5 5 means that the richness of harmonic structures is reduced. For instance, if a major chord moves across the guitar so the tonic falls on successively higher string sets, the structure of the chord in lute tuning does not change. Also, many chords are difficult to play in lute tuning, so a seventh chord is quite difficult to finger. In standard, moving an E chord to the next set of strings makes an A chord, then a D chord; Moving a G chord to higher strings gives a C chord, then F. So standard tuning has 6 different shapes for a major chord, where lute tuning has only one or two.

This shows the principle of least action acts on the guitar topology as a calculus. Action in stardard is far less constrained than lute tuning.

We have here only pitch values, strings, and frets so why isn't that triple a mathematic model?

Perhaps it is this: Mathematicians want to see mathematical proof. But we can hear when pitch is equal, when one pitch is greater or less than another, and when a pitch is multiplied by two.

We know when guitar are in tuning, but we must deduce when they have the same tuning. It would be relatively easy to distinguish guitar in standard and lute tuning, even if they play the same notes. The image of guitar music has the kernal of the tuning.

The topology of music is remarkable because only ordinary math is required to understand the added structure that makes harmony or guitar, but even a brief investigation leads to the realization that the mathematics of music is special and only applies to musical instruments.

I really can't understand why mathematicians and physics are not interested in music as a formal object of study. Doesn't it bug you when you can't understand an everyday object like guitar?

Dear Colleagues,

I've just prepared small portion of code in APDL that builds a simple specimen. It uses geometrical symmetry and VGLUE command. And here is my question: i am not sure if vglue is the same thing as Share topology. Can anyone help and explain whats the difference? The other question is related with VSYM command. I've noticed that when i tried to combine my solids into one solid with vadd,1,2,3,4 command, the edges in geometrical model still exist. Is there any (more efficient) substitution for vadd command to combine my solids into one and removing imprinted edges?

Here is my code:

FINISH

/CLEAR,START

/PREP7

k,1,0,0,0

k,2,15,0,0

k,3,15-((100*3**(0.5))/32),100/32,0

k,4,0,100/32,0

lstr,1,2

lstr,2,3

lstr,3,4

lstr,4,1

al,all

pcirc,5,,0,90

aadd,1,2

/pnum,area,1

aplot

csys,wp

wpcsys,1,0

wpoffs,0,2*100-0.5*100,0

pcirc,100/6,,-90,90

wpcsys,1,0

rectng,0,100/2,0,2*100

/pnum,area,1

aplot

voffst,1,-7

voffst,2,-7

voffst,3,-7

/facet,wire

/pnum,area,0

/pnum,volu,1

vplot

vsbv,2,1

vsbv,4,3

/facet,norml

vplot

allsel

vsym,y,1

!/facet,wire

/replo

vsel,s,volu,,1,2,1

cm,objetosci,volu

allsel

vsym,x,objetosci

cmdele,objetosci

vglue,all ! ShareTopology??

ET,1,SOLID187

esize,005

vmesh,all

vplot

Protein-Ligand Complex was generated after performing site-specific docking in AutoDock 4.2.

I am following the MD-Tutorials by Justin Lemkul.

Often bulky antibiotics are administered for therapeutic purposes. For building topologies for protein and ligands, both are separated using the 'grep' command.

When the ligands are visualised in Avogadro, sometimes the ligands seem broken or distorted thereby unfit for topology building.

I'm Using GROMACS 2020.1, CHARMM force field (Feb 2021), CGenFF server for building ligand topology.

Kindly provide some suggestions to resolve the issue.

Thanking you in advance

Hi everyone, I want to start the discussion about what is the basic concepts, uses, benefits, finding and open problems in the field of Topological Indices. I hope you can contribute to the discussion.

I am working on topology optimization for photonic devices. I need to apply a custom spatial filter on the designed geometry to make it fabricable with the CMOS process. I know there exist spatial filters to remove the pixel-by-pixel and small features from the geometry. However, I have not seen any custom analytical or numerical filters in the literature. Can anyone suggest a reference to help me through this?

Thanks,

I am seeking a pdf or doc file . #Molecular_Dynamic_Simulation #Gromacs #Protein-Protein MDS Hey, I am working on a project where MD simulation is needed for protein-protein interaction in a dynamic nature. I have previous experience of doing protein-ligand MD simulation from Lemkul's tutorial. Now I am facing a few problems, including 1. In the protein-ligand case, first build the protein topology and then the ligand's one. In the ligand topology generation section—another server used to obtain itp files and introduce them to the protein topology file— In protein-protein MDS, what should we do? Where we get the topology of another protein.

By the triplet (X, \tau, I), we mean an ideal topological space, where \tau is a topology on X, and I is an ideal on X i.e., I is a non-empty family of some subsets of X satisfying the conditions (i) \empty \in I, (ii) M \subseteq N and N \in I implies M \in I, and (iii) M \in I, N \in I implies M \cup N \in I.

Given M \subseteq X, M* is calculated as follows:

M* = \{x \in X : U_x \cap M \notin I for every open set U_x containing x\}, called local function of M.

M \subseteq X is called *-perfect if and only if M* = M.

These are prerequisite results that will help to give answer of the question:

For more results and deep concept related to M*, please see the reference:

Dear Colleagues,

Do you know some more or less formalized method(s) to compare topology etc. of two different taxa and some other characters of trees (not tanglegram = congruence of terminal clades). The same for haplotype networks. Question - we have 10 different networks for 10 taxa. Which two of them are most similar I e. in topology... ?

With best wishes

Alexey

I tried to create the topology with PRODRG but it shows that it contains a unknown metal atom Cu. The forcefield i am using is gromos53a6.

Hello Collegues.

I am working on differential systems, i would like to know what does mean two phase portraits topologically equivalent for the same differential system?

Thank you so much.

If you have for example, 5 different samples, that were sequenced, using 3 different regions, but have realised the one gene region is not powerful enough to resolve it to species level, so you add two more genes to better the topology of the phylogenetic tree

I am aware of the facts that every totally bounded metric space is separable and a metric space is compact iff it is totally bounded and complete but I wanted to know, is every totally bounded metric space is locally compact or not. If not, then give an example of a metric space that is totally bounded but not locally compact.

Follow this question on the given link

I am currently working on membrane protein topology research with fluorescent protein. I found so many type I membrane protein signal peptide (SP), like PDGFR or GPI domain, but very few type ii SP. I wonder if anybody could recommend some good type II membrane protein signal peptides. Thank you so much.

Fatal error: Topology include "jz4.itp" not found during P-L MD in GROMACS. But as per procedure i have added the itp file in topol.top file.Please help me resolve the same.(attached)

I am trying to generate OPLSA topology for LiTFSA using LigPargen tool. But it is showing an error. Are there any other tools for generating OPLSA topology parameters in Gromacs?

I'm running 100 ns long MD simulations of a small peptide in isolation or bound to a partnering protein. My goal is to produce a plot of the residues in double helical form from start to end along with a video of the structure using Chimera.

The steps I take after a MD run are...

Step 1:

Center the trajectory file:

gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -center

--- Type 1 for protein and then on the next prompt 0 for system.

Step 2:

Calculate the back bone rmsd of the entire complex:

gmx rms -s em.tpr -f md_0_1_noPBC.xtc -o rmsd_xtal.xvg -tu ns

--- Type 4 then 4 for backbone RMSD calculations

Step 3:

I then make an index file of the two chains:

gmx make_ndx -f md_0_1.gro -o index.ndx

--- Type "splitch 1" hit enter, type the number of what chain I want to reference (typically "2"), then type "q" to exit

Step 4:

From there I want to produce a trajectory file (.xtc) from the index and an updated topology (.tpr) file from my MD run using the index file:

Step 5:

Trajectory of just chain 2:

gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -n index.ndx -o chain2_traj.xtc

--- Type the chain I want to reference (typically "19")

Step 6:

Topology of just chain 2:

gmx convert-tpr -s md_0_1.tpr -n index.ndx -o md_chain2.tpr

--- Type the chain I want to reference (typically "19")

Step 7:

I then center the updated files:

gmx trjconv -s md_chain2.tpr -f chain2_traj.xtc -o chain2_traj_noPBC.xtc -pbc mol -center

--- Type "1" then "0"

Step 8:

I then perform my analysis using dssp and rms

gmx do_dssp -f chain2_traj_noPBC.xtc -s md_chain2.tpr -sc scount_chain2.xvg -o ss_chain2.xpm -dt 10 -sss H

--- Type "5" for mainchain

Step 9:

gmx rms -s md_chain2.tpr -f chain2_traj_noPBC.xtc -o rmsd_xtal_chain2.xvg -tu ns

--- Type "4" then "4" for backbone rmsd

*** The issue I run across is when I open the tpr and xtc files in Chimera with the MD viewer, the peptide is completely wrong. What I've deduced is that the topology (tpr) file for some reason gives each atom in the first few residues their own residue id's. Thus residue 1 actually makes up residues 1-9 (or something similar). However, when I produce a pdb from the trajectory file (.xtc) with:

'''

gmx trjconv -s md_chain2.tpr -f chain2_traj.xtc -dt 100 -o trj.pdb

'''

The peptide is correct. So I believe the issue is that the topology file is being produced improperly due to a bug or something wrong with my steps above. I've also tried using the em.tpr file for input on step 6, but I run across the same issue. This is happening with several different peptides. One peptide that is 65 amino acids long and one that is 18 amino acids long. On the 65mer, it appears to only happen on the first 4-5 residues. ***

As asphalt has various components, how do we create a topology for asphalt.?