Trust me, my cat doesn't use learning decision trees, mobile navigation or finite-state machine models when trying to evade me or get into various trouble. And her processing power is pretty dim compared to a computer. Maybe it's time to start looking simpler solutions. Like rules based behavior.
It's fairly normal practice for the author (or the author's institution) to pay the publisher for publishing the article - not the other way around. This, however, isn't paying a kickback, like, "yeah my article sucks, but here's $100 if you publish it anyways". There are so many articles and publishers own so many journals that they'd probably go broke. It's not like this is Reader's Digest; the audience is pretty much limited to academic institutions.
It's more accurate than what most people believe because they spend so much time jerking each other off.
That's the big variational transistion state theory guy, right? Pay special attention to the details of how those potential energy surfaces are contructed - especially from the groups at that university. All of their QM/MM results match experiment almost perfectly (because after doing a QM/MM simulation they either "correct" the resulting "potential of mean force" curves or "correct" the effective PES obtained from simulation such the corrections cause the correct answer to be obtained.) In other cases, they parameterize the models until they get the answer that they wanted to get.
Wanted to get X, but get Y. OK. Let Z=(X-Y) and call Z a correction. In most any context, it's called cheating, but for QM/MM, it's the norm.
"This is the scientific study of biological processes in terms of quantum mechanics and it uses today's high-performance computers to precisely model these processes."
Precisely modeling these processes? Biggest overstatement EVER. Total hype. When looking at large systems you are screwed and you can generally screw yourself in 1 of 2 ways: 1) Preciesly model few configurations, in which case, your results are not comparable to reality, which is an ensamble average over billions of configurations 2) Model things in an emprirical/semi-empirical, yet surprisingly CRUDE way: allowing one to sufficiently sample phase space, but not in an analytically useful way.
Quantum mechanics in biological systems are typically done with QM/MM, where the "QM" is semi-EMPIRICAL, i.e., it takes parameters. These methods and parameters were NOT designed with biological systems in mind. They were chosen to reproduce small molecule heats of formation. People have found that they work poorly for biological studies unless they are reparametrized (quite frankly, you need to know "the answer" in order to get "the answer" "right") or unless other post-priori, ad hoc corrections are applied. Only a small portion of people who use QM/MM actually reparatrize the semiempirical method and those who do find the new parameters are not very transferable for use between different types of biological systems. For crying out loud, most semiempirical hamiltonians don't even provide the functional forms needed for some of the most basic molecular interactions, e.g., London dispersion, proper polarization to external fields, hydrogen bonding, orthogonalization errors in torsional barriers, etc..
This stuff isn't really new and it's extremely overhyped.
If they came out with something like this, it would be nice if they offered C and Fortran compilers that were specifcally tuned to take advantage of their new technology. Maybe I'm just too picky, but I don't think it's unreasonable to think that a chip maker provide offerings tuned specifically for their chips.
Does this have any implications on the density of mass? When I think of things spinning around a center (e.g., the center of a galaxy), I think of a centrifuge. In a centrifuge, the matter is segregated by density (denser objects move to the outside). So, is it possible then to argue that the lighter stars (although lighter) are more dense than the heavier stars? I guess it depends on the magnitudes of the various forces. Everything is on such a scale that I can't even guess what forces are dominant; however, everything is happening on such a large time-scale that it's unclear to me if even non-dominant forces can play a significant role.
If your system is pure MM and described by point charges (no higher order multipole moments included, e.g. the TINKER force field), then particle mesh ewald will get you the interaction energy between the "real" unit cell and all possible images of that cell. There is still, of course, the real space interactions WITHIN the cell and these either use a cutoff function or some people use recursive bisection/fast mutipole methods (which is much better and can be applied to non-periodic systems -- Look for papers by Perez-Jorda. Er. His last name is hyphenated; it's not 2 people.).
If your MM model contains more than monopole functions, then you are "kind of" screwed (according to one of the developers of the TINKER package) -- Look for papers by Jay Ponder.. he has probably the most advanced MM force field out there. No "good" PME nor FMM scheme has been worked out to handle this.
If your system has a QM region within it, well, I've only known one person to use PME with that... because he's sitting next to me and was the person who implemented it into CHARMM and AMBER a couple of months ago:) (The QM atoms are just treated as points with the mulliken charge). -- Look for papers by Jaili Gao.
>Nonsense. There are a range of parameter sets you use depending on the simulation you want to perform. For example, there are a wide range of models that are used for water alone! (such as SPC, TIP4 etc.)
You are right in that the AC is speaking nonsense; however, he was refering to QM, whereas the models you have listed are not quantum mechanical.
The predominate "QM" models used in simulations are based on the NDDO or MNDO approximation. People hear that they are "quantum mechanical" models and figure "Gee, it's QM - it MUST be right". WRONG! The NDDO/MNDO models are little more than glorified dissociating force fields... in fact, since you mention water, the MM water models that you mentioned would yield far superiour liquid phase thermodynamic properties than the NDDO/MNDO QM models.
People (hell, I) give MM a hard time because they cut off the interactions based on distance and then later realize that doing so causes secondary and tertiary structural artifacts, but NDDO/MNDO QM methods don't include some of the forces AT ANY distance, e.g., London dispersion forces!! Nor do they treat torsional angles correctly (they lack orthogonalization of the basis in the Roothaan equations), etc... but people hear "QM" and they don't bother to check what's under the hood.
PME is for inter-lattice interactions, smarty pants - not the real space interactions. Gee, lot of good that's going to do for a stochastic simulation:/ - sarcasm.
Let me get this straight, they include long-range electrostatics by cutting them off?...and that makes sense to you?
"Force, however, is calculated using a coarse, empirical function of atom positions and their chemical properties."
You give them too much credit... force field people compute *some* of the forces and ignore most of them. Long-range electrostatics are often omitted entirely (and people wonder why their RNA strands fall apart once it flops around a bit - I mean jebus, people!).
People do these simulations to "gain atomic level insight" into the problem; however, it's very rare to hear anyone say anything "insightful" about the chemistry AND do it in a believable way.
More "fascinating" simulations involve including a small region which is treated "quantum mechanically" and thus allow for bond formation/breaking; however, the QM models are so crude themselves that they need to be parameterized to get the "correct" answer. That's right - you heard it. It's the big secret. In order to get the more "trustable" simulations to produce something in the ballpark of remotely representing reality, you have to know "the answer" before you do the simulation and then teach the model to reproduce that "answer"... then you can write a paper and show that you're model "get's the answer" - and that's about the limit of "insight" that's often gained from these sort of simulations.
You know? I saw that one, but that one has thumbnail pictures of each page. I basically want something more...basic. Just the title of the page. Plain text. Exactly like the history/bookmarks sidebar. I tend to have a lot of pages open and they all kind of look alike, so pictures would just make it take up more space and more difficult to quickly jump to the page that I'd want to jump to:)
I like tabbed browsing. I don't like the fact that when I have many tabs that they shrink and I can't read the page titles on the tabs.
I don't want my tabs to show up as tabs - I want them to show up in a side bar. Then I can choose how much screen realestate I use for the side pane and I can make it wide enough to read all the titles if I want.
They almost have this already - I mean, they have a history side bar - it seems like it would be trivial for them to make a sidebar for tabs.
TFA says that the word "metathesis" comes from the words "meta" and "thesis", so the reader could easily read the word as met.a.THE.sis (long E and emphasis on 3rd syllable); however, the only pronounciation I have ever heard is me.TaTH.e.sis (short a and emphasis on the 2nd syllable). Just FYI.
The other $123 went towards buying the hammers and wrenches that they claim to spend $500 for - which they don't - those $500 aren't spent on the hammers and wrenches - it is actually used towards funding the stuff that they are trying to keep secret in the first place. It shouldn't be much of a secret though that the secret is this crazy scheme of keeping secrets.
OK. I posted the same link 5 minutes before you did, but your ID is much smaller than mine. Now I'm more interested in how the mod points will be distributed than the damn link itself.
Slashdot Mirror
Trust me, my cat doesn't use learning decision trees, mobile navigation or finite-state machine models when trying to evade me or get into various trouble. And her processing power is pretty dim compared to a computer. Maybe it's time to start looking simpler solutions. Like rules based behavior.
...or aiming at your cat.
It's fairly normal practice for the author (or the author's institution)
to pay the publisher for publishing the article - not the other way around.
This, however, isn't paying a kickback, like, "yeah my article sucks, but
here's $100 if you publish it anyways". There are so many articles and
publishers own so many journals that they'd probably go broke. It's not
like this is Reader's Digest; the audience is pretty much limited to
academic institutions.
It's more accurate than what most people believe because they spend so much time jerking each other off.
That's the big variational transistion state theory guy, right? Pay special attention to the details of how those potential energy surfaces are contructed - especially from the groups at that university. All of their QM/MM results match experiment almost perfectly (because after doing a QM/MM simulation they either "correct" the resulting "potential of mean force" curves or "correct" the effective PES obtained from simulation such the corrections cause the correct answer to be obtained.) In other cases, they parameterize the models until they get the answer that they wanted to get.
Wanted to get X, but get Y. OK. Let Z=(X-Y) and call Z a correction. In most any context, it's called cheating, but for QM/MM, it's the norm.
"This is the scientific study of biological processes in terms of quantum mechanics and it uses today's high-performance computers to precisely model these processes."
Precisely modeling these processes? Biggest overstatement EVER. Total hype.
When looking at large systems you are screwed and you can generally screw yourself in 1 of 2 ways:
1) Preciesly model few configurations, in which case, your results are not comparable to reality, which is an ensamble average over billions of configurations
2) Model things in an emprirical/semi-empirical, yet surprisingly CRUDE way: allowing one to sufficiently sample phase space, but not in an analytically useful way.
Quantum mechanics in biological systems are typically done with QM/MM, where the "QM" is semi-EMPIRICAL, i.e., it takes parameters. These methods and parameters were NOT designed with biological systems in mind. They were chosen to reproduce small molecule heats of formation. People have found that they work poorly for biological studies unless they are reparametrized (quite frankly, you need to know "the answer" in order to get "the answer" "right") or unless other post-priori, ad hoc corrections are applied. Only a small portion of people who use QM/MM actually reparatrize the semiempirical method and those who do find the new parameters are not very transferable for use between different types of biological systems. For crying out loud, most semiempirical hamiltonians don't even provide the functional forms needed for some of the most basic molecular interactions, e.g., London dispersion, proper polarization to external fields, hydrogen bonding, orthogonalization errors in torsional barriers, etc..
This stuff isn't really new and it's extremely overhyped.
If they came out with something like this, it would be nice if they offered C and Fortran compilers that were specifcally tuned to take advantage of their new technology. Maybe I'm just too picky, but I don't think it's unreasonable to think that a chip maker provide offerings tuned specifically for their chips.
Does this have any implications on the density of mass? When I think of things spinning around a center (e.g., the center of a galaxy), I think of a centrifuge. In a centrifuge, the matter is segregated by density (denser objects move to the outside). So, is it possible then to argue that the lighter stars (although lighter) are more dense than the heavier stars? I guess it depends on the magnitudes of the various forces. Everything is on such a scale that I can't even guess what forces are dominant; however, everything is happening on such a large time-scale that it's unclear to me if even non-dominant forces can play a significant role.
TV really might cause autism?
Heh. Call me back when it definitely maybe causes autism. Otherwise, don't bother me with these shenanigans.
"Yes, but the Daily Show is not SUPPOSED to have "substance". It's on the COMEDY CHANNEL for chrissakes."
I kind of thought that it WAS supposed to have substance... I mean, isn't that part of the joke?
PDP-10
WAS: Programmed Data Processor model-10
NOW: Pedophiles Dig Preteen models ~10
Seriously, WTF?
If your system is pure MM and described by point charges (no higher order multipole moments included, e.g. the TINKER force field), then particle mesh ewald will get you the interaction energy between the "real" unit cell and all possible images of that cell. There is still, of course, the real space interactions WITHIN the cell and these either use a cutoff function or some people use recursive bisection/fast mutipole methods (which is much better and can be applied to non-periodic systems -- Look for papers by Perez-Jorda. Er. His last name is hyphenated; it's not 2 people.).
:) (The QM atoms are just treated as points with the mulliken charge). -- Look for papers by Jaili Gao.
If your MM model contains more than monopole functions, then you are "kind of" screwed (according to one of the developers of the TINKER package) -- Look for papers by Jay Ponder.. he has probably the most advanced MM force field out there. No "good" PME nor FMM scheme has been worked out to handle this.
If your system has a QM region within it, well, I've only known one person to use PME with that... because he's sitting next to me and was the person who implemented it into CHARMM and AMBER a couple of months ago
>Nonsense. There are a range of parameter sets you use depending on the simulation you want to perform. For example, there are a wide range of models that are used for water alone! (such as SPC, TIP4 etc.)
You are right in that the AC is speaking nonsense; however, he was refering to QM, whereas the models you have listed are not quantum mechanical.
The predominate "QM" models used in simulations are based on the NDDO or MNDO approximation. People hear that they are "quantum mechanical" models and figure "Gee, it's QM - it MUST be right". WRONG! The NDDO/MNDO models are little more than glorified dissociating force fields... in fact, since you mention water, the MM water models that you mentioned would yield far superiour liquid phase thermodynamic properties than the NDDO/MNDO QM models.
People (hell, I) give MM a hard time because they cut off the interactions based on distance and then later realize that doing so causes secondary and tertiary structural artifacts, but NDDO/MNDO QM methods don't include some of the forces AT ANY distance, e.g., London dispersion forces!! Nor do they treat torsional angles correctly (they lack orthogonalization of the basis in the Roothaan equations), etc... but people hear "QM" and they don't bother to check what's under the hood.
PME is for inter-lattice interactions, smarty pants - not the real space interactions. Gee, lot of good that's going to do for a stochastic simulation :/ - sarcasm.
...and that makes sense to you?
Let me get this straight, they include long-range electrostatics by cutting them off?
When doing MD, you already know that the cat is dead :(
"Force, however, is calculated using a coarse, empirical function of atom positions and their chemical properties."
You give them too much credit... force field people compute *some* of the forces and ignore most of them. Long-range electrostatics are often omitted entirely (and people wonder why their RNA strands fall apart once it flops around a bit - I mean jebus, people!).
People do these simulations to "gain atomic level insight" into the problem; however, it's very rare to hear anyone say anything "insightful" about the chemistry AND do it in a believable way.
More "fascinating" simulations involve including a small region which is treated "quantum mechanically" and thus allow for bond formation/breaking; however, the QM models are so crude themselves that they need to be parameterized to get the "correct" answer. That's right - you heard it. It's the big secret. In order to get the more "trustable" simulations to produce something in the ballpark of remotely representing reality, you have to know "the answer" before you do the simulation and then teach the model to reproduce that "answer"... then you can write a paper and show that you're model "get's the answer" - and that's about the limit of "insight" that's often gained from these sort of simulations.
360?
...And the number of consoles manufactured! ...And the amount you have to pay for it!
It's the number of degrees in a circle!
You know? I saw that one, but that one has thumbnail pictures of each page. I basically want something more...basic. Just the title of the page. Plain text. Exactly like the history/bookmarks sidebar. I tend to have a lot of pages open and they all kind of look alike, so pictures would just make it take up more space and more difficult to quickly jump to the page that I'd want to jump to :)
I like tabbed browsing. I don't like the fact that when I have many tabs that they shrink and I can't read the page titles on the tabs.
I don't want my tabs to show up as tabs - I want them to show up in a side bar. Then I can choose how much screen realestate I use for the side pane and I can make it wide enough to read all the titles if I want.
They almost have this already - I mean, they have a history side bar - it seems like it would be trivial for them to make a sidebar for tabs.
But what if they fed the chips to the starving kids?
GCC is bigger than Jesus!
Maybe I'm really old but I thought RADIO was killing newspapers.
And while I'm at it, I thought video was killing the radio.
Wouldn't that mean that the internet is killing the video star?
I do more than vote. I vote and kick baby kangeroo's. They're called kangeroo's over there, right?
How could someone post a giant, hires image of the earth and NOT post an obligatory pov-ray "Earth marble" in space?!
// GENERATE WITH
// povray +W640 +H480 +A0.3 -J +Q11 +R6
#include "textures.inc"
camera {location 8 look_at 0}
light_source { -50 color rgb 1 }
light_source { 50 color rgb 1 }
sphere
{ 0, 4.5 pigment {image_map {
jpeg "world.topo.bathy.200405.3x5400x2700.jpg"
map_type 1 interpolate 2 } }
finish {ambient 0.4 diffuse 1 specular 0} }
sphere {
0,1 texture { Starfield scale 1} scale 200
no_shadow hollow on }
TFA says that the word "metathesis" comes from the words "meta" and "thesis", so the reader could easily read the word as met.a.THE.sis (long E and emphasis on 3rd syllable); however, the only pronounciation I have ever heard is me.TaTH.e.sis (short a and emphasis on the 2nd syllable). Just FYI.
Don't let the figures fool you.
The real figure is $3:$1.
The other $123 went towards buying the hammers and wrenches that they claim to spend $500 for - which they don't - those $500 aren't spent on the hammers and wrenches - it is actually used towards funding the stuff that they are trying to keep secret in the first place.
It shouldn't be much of a secret though that the secret is this crazy scheme of keeping secrets.
Got it?
OK. I posted the same link 5 minutes before you did, but your ID is much smaller than mine. Now I'm more interested in how the mod points will be distributed than the damn link itself.