211118 rMD Meeting Protocol

[ehhartmann]

As discussed in today's meeting, the meeting protocol will mainly cover key decisions

User Friendliness

• We should aim to make kimmdy accessible to a general userbase
• Making it possible to use different force fields is desirable but expected to be a huge task and is therefore postponed

I/O

• For now, the user should supply a structure and topology file, as well as additional MD files, as input
• Individual trajectory files and log files are the general output of kimmdy
  • It is desirable to have options in the configuration that change what data is written in logfiles
• Analysis methods could be implemented in a class later but are left to the individual user as of now

Inner Workings

• The topology changer is possibly dependent on the reaction, which would increase the connectedness of both classes
• The topology changer might also be dependent on the force field used
• Creating a topology changer that does not use pdb2gmx has been acknowledged as a major task
  • It is helpful to keep the atom numbering during topology changes

Directions

• Transferring kimmdy to the new framework as a minimum working implementation is the next big task
• Clean-up and discussion of the minimum working implementation comes next
  • Having clean interactions between the classes is the main goal of this step

Next Meeting

• Host: Kai
• Time: 02.12 2pm

PS.: Please add missing key decisions and comment if you think the key decisions in the protocol differ from what we agreed on in the meeting:)