[gmx-users] g_saltbr

Sarah Witzke sawit02 at student.sdu.dk
Fri Nov 20 14:09:12 CET 2009

Dear gromacs users,

First of all thank you for all your previous help!

I have a new question regarding an analysis of ionic interactions between DMPC lipids and a small molecule with a deprotonated carboxylic acid.
g_saltbr takes as input an .xtc file and a .tpr file and from these files it measures the distance between all charged groups and create the three files min-min.xgv, plus-plus.xvg and min-plus.xvg.
My bilayer contains 128 DMPC molecules each having a positively charge and a negative charge. The small molecule has one negative charge. 
Running g_saltbr -f xxx.xtc -s xxx.tpr -sep -b 100000 -t 0.5 puts the distances between charged atoms in separate files, which is what I would like. But now the files are named like this:
sb-<small molecule>'number':DMPC'number'.xvg
How can I then know whether the small molecule is interacting with a positive atom in DMPC (like plus-min) or a negative atom in DMPC (like min-min)?

One more question is on the distance: From this mail I read that the distance calculated is between the charged atoms, not the COM of the charge group:
Then what about my small molecule with the deprotonated acid? Here the charge of the oxygens is spread on both of then. As is also the charge on the DMPC-phosphate oxygens? How can it then be a distance between atoms, when the charge is spread over several atoms?

Thank you,

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