[brahms-md] r56 committed - Deleted wiki page ELBA through web user interface.
brah...@googlecode.com
Author: orsi...@gmail.com
Date: Thu Aug 25 02:10:51 2011
Log: Deleted wiki page ELBA through web user interface.
http://code.google.com/p/brahms-md/source/detail?r=56
Deleted:
/wiki/ELBA.wiki
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--- /wiki/ELBA.wiki Wed Feb 9 07:36:21 2011
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-#summary The ELBA force field: ELectrostatics-BAsed coarse-grain modeling
-
-= Introduction =
-
-The ELBA force field (implemented in BRAHMS) is the most recent evolution
of ongoing research carried out in the
[http://www.soton.ac.uk/~chemphys/jessex/ Essex group] at the University of
Southampton (UK). The ELBA coarse-grain approach is based on an accurate
representation of the electrostatics and a realistic description of water.
These features, arguably unique amongst the existing coarse-grain
approaches, allow the fundamental physical properties of lipid membranes to
be quantitatively modeled. Moreover, these characteristics also make ELBA
directly compatible with standard atomistic force fields, thus allowing
coarse-grain and atomistic models to be mixed in a dual-resolution fashion.
The new ELBA force field is described in the next section. For details of
the original methodology on which the ELBA model is based, and for the
simulation results obtained so far using BRAHMS, see the following
references:
-
- * Orsi, M., D. Y. Haubertin, W. E. Sanderson and J. W. Essex.
[http://pubs.acs.org/doi/abs/10.1021/jp076139e A quantitative coarse-grain
model for lipid bilayers], Journal of Physical Chemistry B, 112, 802 (2008).
- * Orsi, M., J. Michel and J. W. Essex.
[http://iopscience.iop.org/0953-8984/22/15/155106/ Coarse-grain modelling
of DMPC and DOPC lipid bilayers], Journal of Physics: Condensed Matter, 22,
155106 (2010).
- * Michel, J., M. Orsi and J. W. Essex.
[http://pubs.acs.org/doi/abs/10.1021/jp076142y Prediction of partition
coefficients by hybrid atomic-level/coarse-grain simulations], Journal of
Physical Chemistry B, 112, 657 (2008).
- * Orsi, M., W. E. Sanderson and J. W. Essex.
[http://pubs.acs.org/doi/abs/10.1021/jp903248s Permeability of small
molecules through a lipid bilayer: a multiscale simulation study], Journal
of Physical Chemistry B, 113, 12019 (2009).
- * Orsi, M. and J. W. Essex.
[http://www.rsc.org/publishing/journals/SM/article.asp?doi=c0sm00136h
Permeability of drugs and hormones through a lipid bilayer: insights from
dual-resolution molecular dynamics], Soft Matter (2010).
- * Orsi, M., M. G. Noro and J. W. Essex.
[http://rsif.royalsocietypublishing.org/content/early/2010/12/01/rsif.2010.0541.abstract
Dual-resolution molecular dynamics simulation of antimicrobials in
biomembranes], Journal of the Royal Society Interface, in press (2011).
-
-= The ELBA force field =
-
-== Water ==
-
-== Dioleylphosphatidylcholine (DOPC): ==
-http://www.personal.soton.ac.uk/orsi/images/DOPC_AL_ELBA.png
-
-The atomistic representation (on the left) is taken from Siu et al., J
Chem Phys, 128 (2008). The ELBA coarse-grain representation (on the right)
has been created with the image editor of Google Docs; the electrostatic
features (charges and dipoles) are highlighted in red.
-
-=== Full ELBA force field for DOPC] ===
-
-== Dioctadecanoylphosphatidylcholine (DSPC) ==
-
-== Dioleoylphospatidylethanolamine (DOPE): ==
-
-== Ceramide: ==
-http://www.personal.soton.ac.uk/orsi/images/ceramide_ELBA.png