The Periodic Table

So you give the program a list of paths. The script will auto-compare energies and then cartesian coordinates (RMSD) within a variable set of thresholds.

Martin - マーチン

I am still trying to get that gamess to run properly... arghhh

LordStryker

12:34 PM

If the differences land within the user thresholds, it will say that two structures are connected.

The end product will be a rather generic graphviz input file that can be customized later by the user.

But in the end, a connectivity map is auto-generated.

GAMESS. I've never used that program before :\

Martin - マーチン

@LordStryker I did not understand that O.o

LordStryker

okay so, say you have two minima and a TS

Martin - マーチン

jippp

LordStryker

and you perform an irc (or some poor-man's irc) on the ts

now you have two minima, a TS, and two minima from the irc runs

you provide paths to each of these jobs to the program

and it will compare the energies of the minima to those from the IRC runs

Martin - マーチン

great... wakatta!

LordStryker

12:37 PM

if the energy matches within a certain threshold (i.e. 0.5 kcal/mol), it will say that min1 is connected to TS

of course we will look at the coordinates as well

Martin - マーチン

that sounds great

LordStryker

:) Its certainly been fun coding this up.

Its been slow because I've had to go and learn how to use arrays in csh

Martin - マーチン

certainly more fun than getting gamess to run i guess

LordStryker

I've only ever written things to temp files on the hard drive but that isn't very good practice.

Why wont GAMESS run?

Martin - マーチン

haha... if that is remotely the same as in bash, then well done

LordStryker

12:38 PM

@tschoppi !!

heyoo o/

o/

\o/

o/ \O

/o/

\o\

tschoppi

12:39 PM

wow, some serious discussion going on here

LordStryker

O.o

tschoppi

forgive me for not reading the transcript, I'll just barge in here

Martin - マーチン

well... just a little bit whining from my part

@LordStryker I saw it

LordStryker

:)/-<

:)|-<

:)\-<

dance it up!

tschoppi

Well, somebody is certainly having fun here

LordStryker

12:40 PM

I'm always having fun.

Martin - マーチン

Rule #1

LordStryker

I feel like I'm the only one around here who is ever having any fun.

Geoff doesn't like my Avogadro 2 hype :(

Martin - マーチン

haha... no...

tschoppi

Hmmm... I'm currently studying and really don't feel like having fun

LordStryker

I'm currently coding and I'm having a ton of fun!

tschoppi

12:41 PM

And I'm trying to get into a research group for a semester project and constantly get the feeling they don't want me

Martin - マーチン

Because you put him under pressure

@tschoppi what do you want to do?

LordStryker

No pressure. :(

tschoppi

@Martin-マーチン cheminformatics

LordStryker

why the feeling?

tschoppi

@Martin-マーチン I thought it was going to be this vid

well, because they seem to find excuses to not take me in

problem is, I think it's right up my alley w.r.t. my interests and what might motivate me

also I want to check out the group to see where I want to do my MSc thesis

Martin - マーチン

12:44 PM

I know that feeling

don't give up just yet though

tschoppi

I'll badger the PI until I get a clear response, be it yes or no

Martin - マーチン

PI?

LordStryker

@tschoppi Have the PI drop in here. We'll back you up.

@Martin-マーチン primary investigator

tschoppi

@Martin-マーチン the prof

Martin - マーチン

Okay...

got it

tschoppi

12:46 PM

@LordStryker sweet of you guys... not sure how my internet cred might speak for my workplace ethics and the such, but much appreciated!

LordStryker

@tschoppi Don't you know? Imaginary internet points are worth their weight in gold!

;)

Nicolau Saker Neto

Electrons don't weigh much

LordStryker

Compared to...?

They weigh quite a bit compared to other electrons

Martin - マーチン

o/ Nicolau

Nicolau Saker Neto

Heya Martin and LordStryker

LordStryker

12:48 PM

\o/

\o_

\o/

tschoppi

@LordStryker shouldn't you be coding? seriously :D

LordStryker

:\

Nicolau Saker Neto

Give LordStryker a pair of cyalumes and he can go to a Jpop concert

tschoppi

Quick poll: Who of you uses GPG/PGP encryption for their emails?

LordStryker

I'd totally do it too.

@tschoppi Gee I'd look but I should be coding

Nicolau Saker Neto

12:50 PM

I don't encrpyt stuff, should I be worried?

tschoppi

@LordStryker stop pouting. It's unbecoming of you

@NicolauSakerNeto Dunno... I just feel like the more I encrypt, the more I want to encrypt all the other stuff I still send around in cleartext

Martin - マーチン

@tschoppi Meeee

Nicolau Saker Neto

hunter2

Martin - マーチン

well not encryption most of the time

LordStryker

12345

Nicolau Saker Neto

12:53 PM

Maybe someone gets that reference

LordStryker

bash.org/?244321

Martin - マーチン

as you need people with a key to do that -.-

Nicolau Saker Neto

There we go, LordStryker came through in seconds

LordStryker

Not everyday I run into someone who references hunter2

tschoppi

@Martin-マーチン right; but at least you can auto-sign the hell out of all the messages you produce ^^

@NicolauSakerNeto I had to google that one...

Martin - マーチン

12:54 PM

I doo

Nicolau Saker Neto

Haha

Martin - マーチン

all need to see the gibberish :D

********

Nicolau Saker Neto

So it DOES work, poor guy has been mocked all this time for nothing

LordStryker

bash.org/?4281

Martin - マーチン

Yes absolutely

LordStryker

12:55 PM

See? My dancing guy also comes from bash.

Nicolau Saker Neto

I've seen it around before

tschoppi

I need to try that as well...

***********

huh...

LordStryker

Weird.

Martin - マーチン

try man woman

in bash

lol

it's old, but it amuses me still

LordStryker

No manual entry for woman

Martin - マーチン

12:58 PM

I am the king of ...

...my own computer...

sweden?

yay....

ha

...gamess is working

(for now)

LordStryker

Your computer gives you the illusion that you are king

tschoppi

12:59 PM

congrats!

Martin - マーチン

now I just have to write a script, that allows me to submit O.o

But that's a task for tomorrow

LordStryker

^motto of my life

I kid I kid

Martin - マーチン

To be fair though... it's 10pm already

so that really is no task for today

tschoppi

Oh, right... Japan

LordStryker

@Martin Tomorrow I'll bring back the sun

Martin - マーチン

1:01 PM

Well and on that note... I shall run to the supermarket and try to get some left over sushi...

hehe...

sunrise is in about six hours though...

found that out when i returned from karaoke the other night

LordStryker

I promise to have it back to you in six.

tschoppi

@Martin-マーチン If you ever feel like you need to encrypt something and send it via email:
2C78 9BF2 D960 6225 7631  7AAA 8544 4C67 F544 8927

And enjoy the leftover sushi!

In a pinchi there's always kappu ramen :)

Martin - マーチン

well, i might rejoin the conversation in half an hour :D

LordStryker

We'll be here. :)

Martin - マーチン

@tschoppi If they don't have any sushi any more, that'll be it for tonight :)

exit

darn... wrong window O.o

LordStryker

1:05 PM

haha I do that ALL the time

!vi

:q

ls

etc.

tschoppi

A bad habit I've picked up in with vim is <C-w> for backwards word deletion... Always closes browser tabs on me...

LordStryker

1:17 PM

That feel when you close a dozen tabs in Chrome.

tschoppi

1:33 PM

(sigh) it seems I have stepped on some toes in that group a while back... now I have to repair relations and I'm terrible at inter-human stuff

LordStryker

And how do you know this?

tschoppi

It was mentioned in an email I just got responding to my latest inquiry

I don't know what exactly it was that ticked someone or several off, but it must have been something

Trouble is, I really want to do research in that area. I also have the feeling that my work wasn't too bad, so it must be something less tangible like my behavior (which, granted, may be considered odd at times)

LordStryker

Well I don't know the exact scenario you are in but sometimes it doesn't hurt to tackle these things head on. You could goto the PI and actively bring it up in a very concerned way...

tschoppi

Yeah, I think I'm going to do something along those lines. But not today, I'll have to sleep on this or else I'll only make it worse

LordStryker

You should seek advice from someone closeby that you trust.

tschoppi

1:40 PM

I think I'll talk to my former advisor and see if I can go via him. It's another group that is closely related

Well, thanks for letting me vent here, I'll go for a run or something. I need to get moving, been sitting around all day now

I'll see ye round :)

LordStryker

1:52 PM

peace