Exercises

Classical Simulation of (Bio)Molecular Systems (CSBMS)

Prof. Philippe H. Hünenberger + Prof. S. Riniker + Dr Jozica Dolenc / HS23

Fall semester 2023 (HS23)

18 September – 22 December 2023

Goal

Development of skills to carry out computer simulations of molecular systems

Exercises

The practical part of the course consists of six hands-on exercises, each involving the set-up, execution and analysis of molecular simulations using the GROMOS program and force field. The optimal way of carrying out these exercises is to participate a two-hours weekly session supervised by two assistants in our computer room HCP G24

Organisation

• There are six exercises to be carried out. The exercises are formally independent from each other, but skills acquired at one exercise are assumed to be available for the next. The exercises start on the second semester week. In the first semester week, there will be a short introduction to GROMOS at the lecture.
  
• Each exercise lasts two weeks (see table "Exercise Schedule" below). Typically, week 1 is planned for the set-up and week 2 for the analysis and discussion. The actual computation (simulation) is carried out in-between, using our group PC cluster "beaver"
• Each exercise is documented in a detailed script (distributed in principle at the preceding Tuesday lecture; pdf also deposited in the documents page at this point). The document labelled exercise "zero" (and the associated quickref sheet) describes the computational setup, and is associated with the first real exercise
  
• The optimal way of carrying out these exercises is to participate on both week 1 and week 2 in a two-hours session supervised by two assistants in our computer room HCP G24 . We offer two options for this two-hours block on different days of the week (see paragraph "Exercise Sessions" below) and you can chose the session that fits best your schedule. It is in principle allowed to do the exercises on your own instead or to only come for part of the two-hours blocks, but not recommended (you will spend more time and learn less). In any case, the assistant responsible for a given exercise will be available for you over the two weeks, even outside the two-hours blocks if needed (email, personal meeting)
• For each exercise, you are expected to hand in a short report (if possible, maximum 2-3 pages of text, i.e. excluding the space taken by possible graphs/tables) summarizing briefly your findings and answering some "thinking questions" asked in the script. The deadline for handing in the report is usually one week after closing of the specific exercise (exception: it is shorter for the last exercise, as we want it corrected before Xmas; see table "Exercise Schedule" below)
• The exercises can be made individually or in groups of two students (recommendation: work individually at the computer and, if you want to make a pair, discuss your findings during the course of the session and make the report together)
• The enrolment for the exercises is at the first lecture