periodic boundary conditions in the new order parameter code

[ohsOllila]

Should the jumps over periodic boundaries be removed also for the new order parameter calculation code https://github.com/NMRLipids/MATCH/blob/master/scripts/calcOrderParameters.py or does it take them into account?

[hsantila]

Yes, bonds spanning over boundaries should be removed beforehand. Otherwise an error is raised at line 116.

I'll add a note to the header for now.

[ohsOllila]

Thanks. How about removing the water, which was done before, is it still required?

[hsantila]

I think that was done to save space and/or speed up the analysis, but it is not necessary to get the right results

2018-04-17 17:25 GMT+02:00 ohsOllila notifications@github.com:

Thanks. How about removing the water, which was done before, is it still required?

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[jmelcr]

PBC has to be checked before the use of the script -- there is only a small check for a common bond-length, which would stop the script from running if the bond length is too large (e.g. C - H split by PBC).

You can remove water molecules to save space, but it is not necessary.

[jmelcr]

Jumping of molecules over PBC is not a problem, the molecules only have to be "whole" (or at least the studied moieties).

[ohsOllila]

I removed the water removal from the shell script calculating order parameter in commit https://github.com/NMRLipids/MATCH/commit/88228f5a0f858663d2b03a85906f72e8e91b6144. This makes it more simply and it requires less input files.