@Lord was here?

And I. . .wasn't?

:(

if it was so then there was no talk with him

He's pingable now, that means he at least visited.

this happens as you can see in his profile

BTW @Todd Welcome to our chatroom!

hi, thanks!

@ToddMinehardt is back

Are you back @Todd? O.o

yes - here

i was busy with my day job so had to step out :)

Hullo @Dif!

Good I hope chat's still populated.

I needz to get thirst off my mind.

hellowz guyz...

hello there

hi @diffracteD

how much more tym @inɒzɘmɒЯ.A.M

11 mins.

ok.. time's gonna fly by.. @inɒzɘmɒЯ.A.M

Today I didn't go to Kung Fu class/whatever, but I haven't eaten Sahri.

That makes it a 20 hours' wait.

had your shower @inɒzɘmɒЯ.A.M

?

Nope.

bt what is Sahri ? @inɒzɘmɒЯ.A.M

It's the food we eat before the dry fasting begins.

owkhey !

hellowz @ToddMinehardt@PH13

hi there - nice to meet you

@diffracteD It's usually consumed at about ass o'clock.

@ToddMinehardt Tell us a bit about yourself.

i was reading about suhoor just yesterday - any relation?

@BreakingBioinformatics o/

@ToddMinehardt Yeah. . . Related.

So, @ToddMinehardt where are you from basically...

No, not basically, precisely.

ok, stand corrected ..

4 mins more @inɒzɘmɒЯ.A.M

me? from New Jersey. living in Austin, Texas. registered Democrat, so it's hard living here :) married, no kids. came here for graduate school in 1991, ended up with a master's in geology and a ph.d. in chemistry (theoretical chemical physics). tried to hang in academia (2 postdoc's, UCSF and Princeton), ended up doing machine learning for high-frequency algorithmic trading for a few years. now, doing python-related scientific software dev, which really mostly is web stuff

I asked that basically version from someone, and they said Milky way galaxy. . . I had nothing to say.

@ToddMinehardt Wow.

haha nice

People here usually aren't that open about themselves.

whoa ! @Todd you're a kinda guy...

Except @Martin.

But that's because of sausages.

@diffracteD Huh?

eh, i figure you can google me and find my linkedin profile etc. i'm old enough that i don't leave too many bad digital crumbs out there to find :)

well he got a loads of research expo on him @inɒzɘmɒЯ.A.M

@inɒzɘmɒЯ.A.M It's not like I'm incorrect.

@diffracteD Ahan.

@BreakingBioinformatics Never said you are.

yeah sure @ToddMinehardt

well, i do have to tell people that i am not a native Texan nor do my views echo those you hear about - i just live here :)

@inɒzɘmɒЯ.A.M What is "o/"?

o = head and / = waving arm

@BreakingBioinformatics A hand waving, meaning hullo.

@ToddMinehardt I consider myself liberal by default.

@inɒzɘmɒЯ.A.M Gotcha.

I'm currently in my phd and riddling around computational chemistry and macromolecular structural biology kinda stuff @ToddMinehardt

you here in the u.s. or ??

@PH13 >:| Where are the two hand versions? |o/

nop! i'm from India. @ToddMinehardt

why you have two arms, @inɒzɘmɒЯ.A.M? O_O

@ToddMinehardt @Dif: India. @Me: Iran. @Martin: Japan/Germany.

ah, cool - i worked with a bunch of IIT grads over the years

@PH13 Accident.

got it, cool

@ToddMinehardt HAHAHAHAHAHAHA I AM NOT TELLING!!!!!11!!!!11!

super mutant ninja m.a.

XP

@inɒzɘmɒЯ.A.M

If you don't mind @Todd may I ask you for some suggestions sometime...

sure, keep in mind the last time i did any comp. chem. was 2006

It's totally fine, I'm developing some pythonic algorithms and simultaneously trying to figure out some issues related to macromolecuar chemistry.

@diffracteD I have some experience with computations.

More for biochem though.

ah cool -

i was an AMBER guy, and also a Car-Parrinello guy, in addition to some homebrew for various things...

/me currently invading water.

oh yeah !! @inɒzɘmɒЯ.A.M It's the rendezvous time...

@inɒzɘmɒЯ.A.M Breaking fast?

Crushing it.

I'm actually performing some DFT or mp2 based operations @ToddMinehardt

@inɒzɘmɒЯ.A.M Less than a week!

Yeah.

Although because of my background I was having some issues with the basics.@ToddMinehardt

Only 2 hard days after this.

@diffracteD 2+python=?

Why is the last day easy?

wow @inɒzɘmɒЯ.A.M Eid is approaching...

i was a DFT guy for sure, i'd use mp2 once in while for some Gaussian jobs where i could over HF...

@inɒzɘmɒЯ.A.M twython...

@BreakingBioinformatics Last day is hard; the day before it isn't

@diffracteD See? You're not that bad at basics.

@inɒzɘmɒЯ.A.M o.O

I'm currently interested in weak interactions @ToddMinehardt

?

haha...

that's funny.!

i used car-parrinello for looking at ATP hydrolysis in the active site in myosin - worked very well. that said, AMBER was pretty close...

yeah DFT is goofy

Any comment !

@diffracteD as I said before ... that's not a good choice

Yeah, try ice cream cones instead. . .

K my typing speeds will decrease now. . .I'm eating.

@PH13 yeah! I was trying with 6-31g* too ...

that's the minimum

@inɒzɘmɒЯ.A.M If anyone begrudges you, eat them too.

Eats @Bre

yes, but in case of 6-31g* I'm getting more decreased energies @PH13

honestly don't know about m06-2x - i was using b3lyp with vanderbilt ultrasoft pseudo's at the time -

@inɒzɘmɒЯ.A.M Hey! Not me! I'm perfectly content to let you eat!

@ToddMinehardt :O Ping @Martin!

good old b3lyp ;)

like i said, my info is a bit dated....

@diffracteD more decreased energies than what?

Nah, @Martin here loves B3LYP.

but the ultrasoft pseudo's were perfect for H, C, O, N

than 6-31g @PH13

it's a classic :)

@diffracteD ever heard of basis set limit?

heard about, but not gone through @PH13

pubs.rsc.org/services/images/… @diffracteD

ok, so smaller the basis set higher could be the energy. is it like that, somewhat? @PH13

that's the point

increasing the basis functions will lower the energy down to the so called basis set limit

that's what you would get with a complete basis set

so what's the point ? If I plot the whole set of points I'm getting then the curve pattern should be same but the magnitude of energy will only vary. @PH13

I don't know what exactly you want to calculate on your h-bonds

the extent of geometric dependence nature @PH13

w.r.t single point energy

means what influence the surrounding geometry has to the energy of your system

no, the influence of its own geometry on single point energy variations.

so are you trying to map a force field? SPE @ various positions?

yeah somewhat like that, as far as I have grossly thought. @ToddMinehardt

what do you think ?

i would think you should go with the most complete basis set (as @PH13 says) and make sure that whatever level of theory you use, include polarization functions (dunno re: diffuse for your system)

afk, grabbing lunch

but 6-31g* is the absolute minimum ... you need at least polarized "heavy" elements TT_TT ... don't ruin my comp chem course "knowledge"

oh yeah, 6-31g* is absolutely the least you can get away with

BIAB

Hey @ToddMinehardt can't find you in linkedin, can I get some link ?

so what kind of algorithms you generally develop @Todd

Think he's left.

yeah ! @inɒzɘmɒЯ.A.M so invading successfully completed ?..

Yeah.

so you get water then ice cream ?

No ice cream. :(((

would have been great though !

I haven't eaten ice cream for 1 day! I'm going crazy!

@diffracteD linkedin.com/pub/dir/Todd/Minehardt

don't say too much about ice cream, it's about to get midnight here ...

which one might be among them in link !? What do you think !

The first one, duh~

sent invitation..

the one with the image

no one has the image @PH13

the first has one here

linkedin.com/pub/todd-minehardt/b8/330/164

yeah! got it, the third one in @inɒzɘmɒЯ.A.M's list

Initiated another run of dft with polarized basis set, it gonna take months again. :( @PH13

months?

o.o

@PH13 Apologies, he meant centenaries.

yeah, 'm trying to observe every combination possible to get more data points. @PH13

it is taking long time to complete

if it takes months you should be very sure what you are doing

the longest run I took was somewhat around 900 hrs (opt+freq) ... and that was because I used a basis set that was too huge for my system ... I regret doing this

Last time I attempted to analyze ~100k interactions and it took almost 3 weeks non-stop.

but I compromised with polarization issue as you pointed out.

I don't know how many (heavy) atoms your system has but I don't think that many people do normal dft-stuff at very big systems

you run whatever program on a calculation cluster?

As I'm specifically interested in some particular type of interactions, so my system is not too big.

But it's the numerous amount of atomic configurations taking me time...

I have my own developed algorithm working parallel with dft-computing-package, currently running on 128 cores.

can you just say a number of H and not-H atoms?

means ? I couldn't get that !

the sum formula of your system ... like C6H12O6 for glucose

it's not like that.

ok

I'm taking every atomic geometry possible to form a particular type of H-bond.

in short I can say that.

ok

ok, I think I got it

how stupid a idea can be...

;)

what do you say. ? :)

actually following some literature I got some idea, but I need to get more data points than theirs to validate my idea. That was the concept.

I don't know it in detail so I cannot say anything about it. And even if I'd know more about I wouldn't say something about it because I still have so much to learn ^^

It's alright, I prefer imagine > design >learn >imagine cycle...

btw thanks for pointing out the polarization issue...

:)

I hope it helps ... but don't be mad at me if it just costs time ... whatever you do on your research is your own responsability O:-)

You got a valid point, so I had to follow.

But may i ask something..?

sure

the key factor I have to deal with is directionality in case of H-bonds, and which is mainly because of charge transfer component of this kind of bonds. So, if I used m06-2x functional wouldn't it be possible to get the correct energy ?

as m06 suit of functions deals with charge transfer component very precisely, as per most recent literature.

I fight for a long time with the minnesota functionals and which one to choose ... I never really figured that out ...

I was talking about the combinations basis_set+functional = 6-311g+m06-2x or 6311g*+m06-2x

and the "correct" energy with dft is such a thing. as per theory dft is variational which means you cannot go deeper than the true energy. but as what we do is not dft but dfa and the functionals we use are somewhat empirical this variational stuff doesn't count and as with mp2 you can result in a lower energy than the true energy ... so be cautious about the "correct" energy ... whatever this is

@diffracteD good night

back, should be LinkedIn, got your invite

(to @diffracteD)

took some time to find you :)

@Todd

hah, well, better late than never :)

agreed @Todd

@PH13 Thanks again on the basics !

much appreciated guys ... !!!

shutting my gear down, however any advice is heartily welcome on this topic, 'm currently interested in.

cheers, see you next time!

adios

@inɒzɘmɒЯ.A.M

entertain me

Yes?

OK.

Entertains @PH13

:D

Why are you bored?

because I have to track bacteria

Where? Mars?

from videos

they have been recorded and I have to follow them and save their paths

Oh, so it's like the snake's game?

not really ... more like point and click adventure

but without the adventure

I wonder how boring it is.

6.022*10^23

approximately

Hey, do yourself a favor, go to the newest questions on chem page 100, and start flagging comments.

why should I?

For the badges.

Better than chatting with a molecule

I really have to track those bacteria ... :C

What'd happen if you don't?

then I won't get my master :O

Wow. . .

Thinking about a way to distract @PH13 from watching those bacteria

:P

you like my beautiful colored new question?

Can you replay the video in case you've missed something?

@PH13 Link?

Oh, the orbitals' question?

indeed

It was beautiful, but I downvoted an hour before 'cuz you didn't talk about my orbitals there. :(

your two beautiful orbitals? ( Y ) ?

Yes. And I'm male. They're called handsome.

as you train a lot it's maybe even cup size B

OK I see where this conversation is gonna lead to. . .

BTW how can you chat and track 'em at the same time?

I'm converting the video first

videos

Oh. . .To a .bacteria file format?

.bct :P

Seriously though, are you converting them to cinema quality? Will you sell tickets? Will bacteria know their arts are being exhibited and sold?

with the nsa 144p->ultra hd converter, yes ... and no, they are my slaves not knowing that they are sold

This is outrageous! I'm gonna write a report to UN, and you can't catch me!

I'll catch you if I can

Bacteria rights are violated here.

@PH13 Oh, really? We'll see about that.

muhahahhahaha

your profile info is obsolete "Should anyone care, that's a cyclohexane, not a simple hexagon or anything."

Cough cough clears voice: Ahem, I hereby declare your arrest according to code 13 in correlation of violation of bacteria rights code 0XFFF3362 of the United Nations' database. You are under arrest, sir, and anything you say might be used against you as balloons in the court. Guards, seize him.

@PH13 Riiight, I was thinking about it earlier yesterday. . .

somehow not how I mentioned it to be

A space before the asterisk and what it's supposed to work on stops it from italicizing.

next time

We have seized you, yet you have no idea. . . Bring him to the Matrix. . .

^^

Now you wait and see what happens next time you sleep.

when am I able to ping someone?

Who's someone?

someone who's only right now on chem.se

Thou can't unless they visit chat.

On another note, you can invite them to chat in the form of a comment.

ah ok

I'm guessing you wanna invite Brian?

geoff

but I will talk to him over mail

Ahan.

About Avogadro?

indeed

about FAILING avogadro ;D

no .. more about me failing to use it properly