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: http://lists.gromacs.org/pipermail/gmx-users/2005-June/015811.html 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, Sarah -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
