Study Group

The goal is reading, word by word, more than 60 papers in three months about predicting the binding free energy of interacting molecules by means of the MM/GBSA method.

Some rules to be all on the same page:

• The file 'Name-of-student.md' has a tentative guide with a list of papers to be read in order. Week by week the file has to be updated if additional papers were read.

• After reading a document, the student will open a new issue in this repository with the corresponding document-keyword as title. The body of the first post in the issue will contain the bibligraphic reference together with three or four lines giving a breaf summary with those ideas the student wants to highlight. After that, tags will be attached to the issue with those words describing the work reported in the document.

• Papers, proceedings and book chapters will be named with a key string made up of the first author's family name, the publication year, the first word of the title, and an underscore followed by the first and last characters of the string after the last "/" symbol in the DOI. For instance, the paper entitled "Why me?" written by John Doe, published in 2020 with DOI "10.137/journal.x.30522" will be referred to hereinafter as 'Doe2020Why_j2'.

• Preprints deposited in the arXiv will have a key as if they were a published paper. But instead of taking the last two characters of the key from the DOI, they will come from the arxiv ID in a similar way (first and last character from the ID numbers after the '.' symbol). As such, the preprint entitled "Why you?" written by John Doe in 2020 with the id arXiv:1501.05235 will be denoted as 'Doe2020Why_05'.

• Thesis will be named with a key string consisting of the string "Thesis:" followed by the first author's family name and the publicacion year. This way, the thesis written by John Doe in the year 2020 will be referred as 'Thesis:Doe2020'.

• Don't be shy to share ideas and doubts either in the issues board or in the discussions area. It is good to have a written history of the learning process.

Tips for the young researcher.

Is this your first research work? If you are at the begining of your scientific career, let us share with you some tips before you start your readings:

• The main purpose of this exercise is understanding, not just knowing.
• Keep in mind from day one the open questions you already have. Be smart to indentify where the answers could be from the first paper you read.
• Do not feel overwhelmed the first days. Avoid running crazy after every single doubt. Don't try to check every reference in your first paper.
• Write down in your list new questions and doubts. Long term, having many doubts it is more effective than having a lot of answers.
• Work first building a good and consistent structure of doubts.
• Work later in having a good and consistent conceptual story covering all your doubts. Fill the gaps reading, searching and thinking, as if it were a detective work. The mist will vanish with time.
• You will probably have hundreds of ideas: Why this question was not approached? Why this is not done? What would happen if...? Write down all these ideas, they are gold, they can be the seed of your future scientific contributions.
• Having a big collection of unread papers in your computer doesn't make you smart.
• Having a big collection of unread papers in your computer doesn't mean you understand the topic.
• Look for the meaning of the spanish word "adanismo". Do you really think is a good attitude to start a scientific career?
• Spend 10 minutes in internet looking for what the "Dunning-Kruger effect" is. Did you understand the plot confidence vs. knowledge? Where are you now? Where are you going to be in two weeks, and in two years of digging into this topic?
• If you walk 1000 steps and just one, just a single step, any one, was random, you will have no idea where you are at the end of your walk. Do not guess anything. Do not assume anything. Do not advance in your research with out understanding every move you did, every mistake or success you made.
• Enjoy learning. Enjoy suffering too.
• Don't be hasty.
• If, from the beginning, you think everything is simple, be 80% sure you didn't understand a word.
• If after being lost in the mist for along time, working hard to get some clarity, you come up with what you think is a too simple idea to be comunicated, be 80% sure you did a good job.
• If you are not enjoying when concepts begin to fall into place, maybe being a scientist won't make you happy.
• If you are not enjoying when you realize that what made sense yesterday doesn't make sense today, maybe being a scientist won't make you happy.

One last thing. This section is far from being a self-help guide. You can read about the following two empiric principles:

• Hofstadter's Law: "It always takes longer than you expect, even when you take into account Hofstadter's Law".
• Paretos Law: "80% of consequences come from 20% of the causes". Which means that 80% of your time and effort will produce only the 20% of your results.

And you can think: 'Aha... now that I know, I can do better'. Ok, let us tell you something. Let us dare to share with you a last piece of wisdom: no, you can't.

"When nothing seems to help, I go look at a stonecutter hammering away at his rock perhaps a hundred times without as much as a crack showing in it. Yet at the hundred and first blow it will split in two, and I know it was not that blow that did it, but all that had gone before." Jacob August Riis.

Be as stubborn as smart.