sawit02 at student.sdu.dk
Fri Nov 20 14:55:03 CET 2009
From: gmx-users-bounces at gromacs.org on behalf of Justin A. Lemkul
Sent: Fri 20-11-2009 14:25
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_saltbr
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.
Ah, now I understand the comment. Slow Friday. Thank you!
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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