Tuesday, 30 October 2012

Can we do Science at home... Is it even possible?

Heya folks,

Most people associate research and all things science to the laboratory. And they think the laboratory is the place where all the scientists and research go and use all sorts of expensive, high tech gadgets to conduct studies that possibly impact our lives. Is it really true?

Well, its mostly true. Some experiments have to involve machines that are huge and cannot be easily moved around, such as the Nuclear magnetic resonance machines as well as the infra-red and ultra violet spectrometers.  However, computational based chemistry utilized servers that can be hosted in any part of the world. Which means, anyone can get access to them and start an experiment as long as you have access to the internet. For smaller scale simulations, you can actually do them on your own laptop or desktop computer.

So, yes. You can do scientific research in the comfort of your own home! Its easy to get started if you have the appropriate tools and software license in your college or company. Alternatively you can always find open-sourced programs that are completely free or available for use for educational purposes.

Let me recommend some in the next post!

signing off~

Monday, 29 October 2012

What EXACTLY is computational chemistry simulations ...?

Heya folks,

This is a question that is commonly asked in the minds of aspiring researchers and students when they are introduced into theoretical or computational based chemistry. Is it easy or hard or just too plain crazy to understand?

Well, computational based chemistry does dabble in quantum mechanics and its definitely a complex subject that require one to be comfortable in fundamental college mathematics before diving straight into it. This is something that freshmen college students might want to think about before picking up a class related to the subject. But I digress ...

In my opinion its a difficult subject made easy with the assistance of modern computers. With continuous improvements by Intel and AMD, our computers are now able to process much more complex information more quickly than before. And this involves solving the infamous Schrodinger equation with some caveats (more discussed soon!). By letting computers handle most of the work, we just need to focus on two things:

1. Tell the computer what to do

This sounds simple but it is essentially difficult. Despite the technological advancements, computers cannot help you do your homework, much less do your research for you without you telling it what to do. Here, we have to prepare the appropriate input settings into the software before performing the necessary calculations. These settings have to be carefully determined and in most cases, sampling tests may only need to be performed initially and not throughout a research project. Although most software has a set of default values, I stress the importance of understanding the individual settings and personalize them because EACH and every chemical reaction or study is fundamental different. Speaking from experience, it feels utterly terrible when you realize you need to make some changes after doing a lot of work. It just slows things down and make you look pain ineffective and unproductive.

2. Designing studies and reactions

Now, this is the hard part. Designing novel studies and research proposals is the bread and butter of not only chemists but scientists in general. It is the most fundamental and critical stage of any research and one which I notice students seem to underestimate until much later.

Having a solid research proposal with clear goals on what to focus upon WILL help you a lot because you have a clear picture of what you need to get done even when you get stressed out and tired during the err ... enjoyable and enriching process of research. Less running around in circles means more productivity and it just makes you seem trustworthy because people know you have a PLAN.

So The question is how to get these ideas since they are so important ... ?

More in my next post ...

signing off~

Sunday, 28 October 2012


Heya folks,

The title says it all, this webpage will be somewhat focused and below are some of the items that I will strive to include on a regular basis.

Some of them such as 'tips and tricks' will be posted as and when I pick up any or when I realise something might be useful to the wider audience. Others such as 'computational stuff/examples' will be a more regular feature and a couple of ' new series' on 'Writing' and 'Getting Published' will be  included gradually.

Updates on upcoming items will be updated regularly, so will recaps. If you missed anything, no worries, you can always find it in my recap posts or under the 'archives'.

Things to look forward to:

  1. Research tips and tricks 
  2. Article reviews
  3. (Useful) website reviews
  4. Computational stuff - examples
  5. How to subscribe to journals
  6. Research : How to do it systematically
  7. Writing tips : How to write systematically, minimize distraction 
  8. Reading tips: How sieve out important information quickly
signing off~

Friday, 26 October 2012

Let's get this blog started

Hey guys JohnHDchem here,

I am a (young?) theoretical chemist and I created this blog because I hope to offer come useful tips for follow novice simulations people who have a headache with the settings, option selections and stuff.

I certainly do not claim to be an expert in any way so the content in this blog are mainly my experiences and stuff which I have learnt from tutorials. If there is any discrepancy with the information, leave a comment and we can all have a discussion.

I intend to post some examples along the way and talk about how they are done. Screenshots and pictures are likely to be included, and maybe videos with commentary in the future.

I mainly work on the vienna ab initio simulations package (VASP), dmol and CASTEP, so information would center around these software packages.

Hoping to post some content soon.

Let's get this blog started