What's the computational chemistry scene like in Boston?
What are the best companies for comp chem and drug design? Big companies like Amgen/Pfizer or are smaller companies better for this?
Should I try to do a postdoc before applying?
Thank you!
Through reading about computational chemistry, it seems like there is a lot of work involving using established programs/packages (Q-chem, Gaussian etc...) and also some work involving method development, and writing one's own code for simulations.
I like the latter two, but not the former. Is a subdiscipline of chemistry that avoids running an excessive number of established packages? I'm more interested in developing the software and the theory than using it to do large numbers of computational experiments. To be specific, I don't mind using other's software, so as long as my work is actually adding code on top of it.
I know theoretical chemistry is a thing but it often gets lumped with computational chemistry. As it turns out, a lot of theoretical chemistry also seems to be running a lot established packages.
Some questions:
- Can someone in the industry tell me what it's actually like?
- Is it actually possible to use computational physics + AI to rationally design medicine?
- What is the success rate or usefulness of computational chemistry in industry?
Im hoping to do work in the service of science, and this field seems cool. When ive looked into it it seems most grad programs are for chemistry people and they learn the computer skills. Wondering if theres a program supportive of people with the computational skills and help them learn the chemistry?
Coming from a mainly practically oriented area of chemistry, I want to get into computational chemistry. So far I've taken additional university courses in quantum chemistry and basics of computational chemistry and started an internship in a group focused on theoretical research. However, I frequently get confused with the amount of different programs to use and their different purposes and suitability, so I wanted to know if there is literature that lists the available tools regarding their purposes, strengths, flaws, and maybe suggest a workflow like "use X to preoptimise, then Y for your energies and Z for vibrations" or something like that (and ideally with an explanation why since I can't stand not knowing why I'm doing something). I know that this heavily depends on the observed system, but maybe there are some rough guidelines at least? As I said, I come from a rather practical field, so most theoretical stuff is new for me and a deep-dive directly into the different forms of wave-functions or fractions of methods A and B won't help me that much as I'd have to google everything anyway. Or does anybody working in TheoChem maybe have some tips on how to build up this basic knowledge? Because currently when reading papers I feel like they want me to run when I can barely crawl.
It explains how to use the most popular libraries and software in a very neat way! I really recommend it. I hope you enjoy it too.
Hi everyone,
I currently work in industry (PhD in chem), doing drug discovery and development. My main focus during my PhD was medicinal computational chemistry, software development, and chemical biology. If you'd like to learn more about any of these fields, or anything else related to research, doing a PhD, going from academia to industry etc. Just write your questions in the comment section and I'll answer as soon as possible!
So i'm on a project where i'll have to calculate the IR spectra of different L-cysteine derivatives. I'm working with Arguslab and gaussian. Now the problem is that i have not found any helpful instructions for the use of either programs or at least i don't really understand them. I have diffictulties with arguslab finding out what i have to do to generate a useable outputfile for gaussian. There are basically no youtube or texttutorials (at least in the languages i understand) that gives any explanation to what i have to do (arguslab has a manual but i have read it twice and ame none the wiser). My labsupervisor and none of the other guys have worked with the program before and can't help me. I'd have to ask my prof but he's out of town untill next week. Then when i have created the correct output file for gaussian what do i do with it? I have done something similar before years ago but i can not remember anything of how i calculated the nmr spectrum back then. (Gaussian and arguslab run on two different computers at the lab. I'm in “homeoffice“ today and am only working with arguslab as i have no unixsystem and gaussian running on my homecomputer). Thanks for any help
Just learned about computational chemistry and it seems like the perfect career choice for me. I have always loved chemistry and people have told me that i would be a good fit for CS. I don’t know if double majoring in these two areas would really lead to me pursuing my interest while also making big bucks.
I am an international student studying in the US and I hope to get a job right after undergrad. How feasible is this? What would you recommend I do?
Hi all.
You're already using some general statistics package for your data analysis. Computational chemistry, so far, covers molecular dynamics, quantum chemistry and reaction kinetics (proprietary and/or open source software).
Any ideas about new software? What would be useful in your lab/work environment? Or, what would you use in your research, that doesn't exist yet?
In need of some advice, I have a choice between AI-ML course at Jain University, Bangalore (4y course) and MSc Chemistry dual at BITS (5y course), which would be optimal considering I would like to take up research in Computational Chemistry? (I also love Biological Sciences, the first incentive was to take up Computational Biology, but I came across programs like Mol Print 2D & 3D and loved the application of CS for studying the properties of different drugs)
I definitely want to go abroad for higher studies, I would've taken up CSE without any hesitation at BITS if I'd scored enough, and gone for masters abroad but since my score was quite low, I'd have to take up Dual at BITS. I'm under the impression that after the master's degree at BITS I'd have to apply for a PhD to further my studies as two masters is unnecessary (?) I'm not sure if that's right?
also could I get any ECE/EEE/ENE at BITS with my score? since I heard that most of the syllabi for CSE and Phoenix branches overlap.
my_qualifications: boards 98.8% JEE mains - around 91 percentile BITSAT - around 280
After all these considerations, which course would be better for me to choose?
thanks for your time!
(I was initially a NEET aspirant, not because I wanted to be a physician, but I loved PCMB until class X and was into biology (human physiology, anatomy, organ systems in general). therefore the idea of going into medical research after MBBS was given to me, but I realised that I had no interest getting a Bachelors degree in Surgery if I was only interested in medicine as a Research prospect, I would still love to take up research in the Biological Sciences but since I have to choose between Research in Biology or Computational Chemistry, I'd have to choose the latter)
Hello everyone, are there any free computational tools that could source for potential small molecule drugs against protein targets in a high throughput fashion? i.e. Using computational models to compare possible small molecule drugs which could target a specific protein. What are commonly used computational tools in medicinal chemistry?
Any input is greatly appreciated!
Hi all,
As the title suggests I am looking to finally dip my toes and mess around with some software or programs used in this area of computational chemistry. I will be applying this year to a PhD, and have seen that I can apply to physics, applied physics, chemistry, pchem..etc PhD, but I would like to do computational research for materials discovery pertaining to energy harvesting, carbon capture, or related topics.
Where is a good place to start? I know python but do not know any object oriented programming or anything like that. I have a basic knowledge in Matlab and Julia as well.
Thanks!
Hi all! I am an undergraduate student in the States majoring in Chemistry and intend to apply for Ph.D. later. This summer, I am working in a computer simulation research lab in a state school and I do enjoy it. Because of that, I plan to pursue a Ph.D. in computer simulation/computational chemistry. However, I don’t know anything about career prospects for a Ph.D. degree in comp chem. Can somebody give me some advice on this problem? I will be really appreciated
Posted originally by
I tend to get a lot of questions about how to learn chemistry online or how to prepare for/supplement university level chemistry courses. So I took a few hours and made a list of the most comprehensive, helpful, and interesting chemistry lecture series. Nearly all of them are recorded in a real college class and are taught by professors. I tried to organize it by sub-branches but the titles of each series should make it pretty obvious as to what type of material the course covers! I'm a huge fan of making college lectures public and hope at least a few of you will find this helpful! Please keep in mind that these are FULL COURSES and that every one of these links is to the first lecture of an entire trimester/semesters worth of courses, so there are generally about 30-40 videos that come after the one that I have linked you to!
EDIT 1: Added Chemical Engineering, Biotechnology, Metallurgy Lectures, Advanced Organic Synthesis: Stoichiometric Organometallic Chemistry, Chemical and Biomolecular Engineering - 179, Intro to Chemical Engineering, Astrobiology and Space Exploration, and a bunch of quantum chemistry/mechanics classes (10-30-14). THINKING ABOUT ADDING PHYSICS, BIOLOGY, MATH, AND MEDICINE CATEGORIES. LET ME KNOW IF THAT WOULD BE APPROPRIATE/IF ANYONE WOULD BE INTERESTED!
EDIT 2: Wow, thanks for my very first Reddit gold! (10-30-14)
EDIT 3: ANOTHER GOLD?!?! Seriously, thank you guys so much! I'll do my best to keep updating this list and adding more subjects! Also realize that this post made it into the top 100 posts of all time on r/chemistry, so that's really awesome! Really glad I can give back to such a helpful and interesting subreddit! (10-30-14)
EDIT 4: I messaged a moderator (u/chemjobber) about getting this stickied/added to the sidebar because of how many of you have requested it. It'll more than likely happen if everyone that would like it stickied messages a moderator about it! (10-30-14)
EDIT 5: Mods added this post to the sidebar of r/chemistry! It's under the Chemistry Links header and titled "Online Chemistry Lectures". Also, I appreciate the feedback and suggestions and will add categories for other subjects as soon as I can find time! (11-2-14)
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... keep reading on reddit ➡I'm currently working on my UG thesis and unfortunately due to this pandemic we cant work on a wet lab so we don't have any other choice but to do a dry lab. My knowledge about computational chem is so little because it wasnt given to us as a subject. Ive only learned from reading some published articles.
It would be much of a help if anyone can help me and guide me about semi empirical molecular modelling. Thank you
Sorry for the broad question haha! To be more specific, what kind of careers does it lead into? What's day-to-day life like working in CC? Do you enjoy it etc.?
For context, during my degree, I've realised I'm horrible at lab work - I generally get terrible yields and sometimes my data is pretty poor, despite 2 years of practice. I love physical chemistry the most, but I feel like I'm not cut out for the experimental aspect.
I still really want to go into science as a career and I need to choose a topic to do my masters project on for my 4th year. My supervisor suggested computational if I'm not very good in a lab, yet I can't help but feel being poor at lab work is going to limit me so much, as surely I can't solely do computation??
Sorry for the rant, but any advice would be much appreciated :)
Hi, I remember seeing a subreddit about comp. Chem. some time ago but I cant find it anymore. Does anyone know anything or have the name of it? Thanks in advance!
Is computational chemistry and drug design a viable career in industry? Does it provide secure job opportunities?
Hey all, I'm just a curious undergrad continuing my self taught plunge into Computational chemistry, and it should come as no surprise that I am interested in physical organic chemistry. Regardless I have obtained the firefly program (I think it's based off of Gamess US), but I really don't have much to do with my results. I've used macmol, however this is totally inadequate considering I can only really see ESPs or maybe Molecular orbitals but I don't think I can use it to get my hands on hard data like bond distance or maybe other things. I don't think it's as urgent or important but I also use avogadro for the inputs and don't know if that can do everything I want it to do (for instance I want to try to guess some transition states) and don't know if I can do it there. Pretty much asking for any easy to obtain or free Computational chemistry programs available
Hey everyone, so I'm a sophomore at my University studying ChemE and in the past few months i have been interested in studying Data science and it has been going on for a while and i want to complement it with Chemistry as a domain. I have reached out to some of the people in my connections and one person told me to look up Computational chemistry saying it will help me to get into the actual implementation of chemistry and also get some exposure into the Research field. So my questions are:
- What are you guys' opinion on this?
- How is the market at the moment?
- Will this part of the chemistry be demandable as time passes?
- Would you recommend going for this particular skillset?
- What else sectors can i look into if It's not the optimal one?
Thank you in advance.
Hello! The documentation and references for gaussian's ONIOM for large molecules guide references reactants and products, however the systems shown as example are a simple 1 step mechanism.
I am trying to model an enzyme catalysis with at least 2 intermediaries.
For such a reaction, should I do SValue validation on the intermediaries too, or is it sufficient to run it on the initial and final states?
I'd ask my supervisor but he's on a vacation until next week, and my labmate has no idea either (his own project was already validated through literature, he just did minor adjustments).
I'm mainly asking as I hope to reduce computation time, as UFF:UFF needed for SValue validation is not that long... It quickly becomes long if I run it for each intermediary (especially since the purpose of my project is to determine what the actual reaction pathway is based on what's been proposed by experimental papers, and that'd be a LOT of options to validate).
I currently do research in comp chem and we do drug discovery type research using md simulations. I would stay in this lab during the duration of my phd. I would eventually like to do computational work that deals with genomics. If I were to get a phd in bioinformatics, would I be prepared to work in this kind of an industry? I did my undergrad in biochemistry so I have some previous knowledge of genomics.
Any help is appreciated :)
About to get my PhD, at an interesting point where I can choose a hardware role at a big tech company, or a computational chemist role at a drug design startup doing molecular simulations.
Computational drug design seems cool and impactful, but is it a viable career? Can you make a living doing it for life, and does it generally yield secure jobs?
I posted something similar about 6 months ago and got no responses.
I have been programming python for 4 years (with a smattering of other languages) and have taken a number of scientific computing classes, and I also have a CS minor.
I am about to graduate from UT Austin and I got into the masters programs at UT Dallas and A&M (potentially more to come). I could also do a second bachelors in CS at UT Dallas.
The only thing I can say I definitely don’t want to do is web development. Which it seems is what most bootcamps target.
Any advice?
if anyone needs compchem software, including but not limited to gaussian, spartan, gamess, mopac, vasp, firefly, hyperchem, schrodinger suite, biovia materials studio.... feel free to pm me, or better still hmu on the drugnerds discord. i am not officially stating i would "share any of these for free", but im sure i can help you out ;)
I'm a materials scientist with a few years of experimental experience in polymer synthesis, but my chemistry knowledge is pretty pigeon-holed to a handful of reactions and whatever I picked up in undergrad intro-to-organic. Is there a good set of material (papers, books, MOOCs, whatever) to read through if I'd like to learn more about computational chemistry?
I'm not sure where to start (I guess maybe going through some further chemistry courses to have more theoretical basis?), and I really don't even quite know what's realistic to simulate with current methods.
I'd like to keep exploring some polymerizations I played with back in grad school, but without access to a lab anymore this seems like it might scratch that itch.
Apologies if this is too basic for chempros.
I'm currently working on my UG thesis and unfortunately due to this pandemic we cant work on a wet lab so we don't have any other choice but to do a dry lab. My knowledge about computational chem is so little because it wasnt given to us as a subject. Ive only learned from reading some published articles.
It would be much of a help if anyone can help me and guide me about semi empirical molecular modelling. Thank you!
I'm currently working on my UG thesis and unfortunately due to this pandemic we cant work on a wet lab so we don't have any other choice but to do a dry lab. My knowledge about computational chem is so little because it wasnt given to us as a subject. Ive only learned from reading some published articles.
It would be much of a help if anyone can help me and guide me about semi empirical molecular modelling. Thank you
Hey everyone, so I'm a sophomore at my University studying ChemE and in the past few months i have been interested in studying Data science and it has been going on for a while and i want to complement it with Chemistry as a domain. I have reached out to some of the people in my connections and one person told me to look up Computational chemistry saying it will help me to get into the actual implementation of chemistry and also get some exposure into the Research field. So my questions are:
- What are you guys' opinion on this?
- How is the market at the moment?
- Will this part of the chemistry be demandable as time passes?
- Would you recommend going for this particular skillset?
- What else sectors can i look into if It's not the optimal one?
Thank you in advance.
)