Writing MDP file and other options in smaller or upper case letters

User discussions
1

Dear all,

I have recently parametrized an alcohol molecule using acpype webserver tool to get amber compatible forcefield parameters. The atomtypes were written all in smaller case letters such as: oh, ch, ho etc. When I am combining the itp with an amber forcefield.itp file no error happens. However, if I am using upper case letters in the itp file like: OH, CH, HO etc., then gromacs reports a warning: “that atomtype OH has been defined earlier in the forcefield files”. I expected to have the repetitive atomtype entry warning for either of uppercase or lowercase letters as I thought gromacs does not differentiate between uppercase and lowercase letters as we often use them in the mdp files.

I was of the impression that gromacs does not distinguish between smaller and upper case letters. For example: in the mdp file using tcoupl = Berendsen or berendsen or tc-grps = System or system: does it really matter or this smaller case and upper case letter is not differentiated in the mdp file but everywhere else e.g., itp or top files uppercase and lowercase letters may actually indicate two different things?

I understand this might be a self-explanatory and a naive question. But I could not find any documentation on the same. Any explanation would be much appreciated, thanks in advance.

2

Indeed there seems to be no documentation.

Everything used to be case insensitive in GROMACS. But as some force field have atom and molecule types which only differ by case (why??), we have made those case sensitive. Chain identifiers are case sensitive when both cases are used. Everything else, including mdp options, is case insensitive.