Sarah Witzke wrote:
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)?
If you omit the -sep option, you'll get plus-min.xvg, min-min.xvg, and
plus-plus.xvg. In these, you will find the different groups that interact
through these different charge interactions.
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?
The program identifies the interacting charge groups within the cutoff
specified, and then prints the minimum distance between any two atoms in the
interacting charge groups, as stated in the thread you quote.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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