[gmx-users] lipid gel phase simulation model building

[Carsten Selle]

Dear gromacs users,

the gel phase of some lipids as the L beta prime of DPPC is
characterized by all-trans alkyl chains which are tilted with respect to
the bilayer normal. I would like to set set up a system analog to the
one described by Venable, Brooks & Pastor, J. Chem. Phys., 112 (2000),
pp. 4822. They used a periodic box which is cubic (39 x 39 x 63 A***3).
I tried editconf and genbox to generate a cubic simulation box and a
suitable aqueous environment for the bilayer I generated from crystal
data. However, since the box is cubic, there is plenty of room for
unwanted water-alkyl interaction. genbox accordingly placed water in
hydrophobic places. The water molecules should (almost) only interact
with with the lipid headgroups and water. Any helpful comment is greatly
appreciated.

Best regards,
Carsten

[Justin A. Lemkul]

Post by Carsten Selle
Dear gromacs users,
the gel phase of some lipids as the L beta prime of DPPC is
characterized by all-trans alkyl chains which are tilted with respect to
the bilayer normal. I would like to set set up a system analog to the
one described by Venable, Brooks & Pastor, J. Chem. Phys., 112 (2000),
pp. 4822. They used a periodic box which is cubic (39 x 39 x 63 A***3).
I tried editconf and genbox to generate a cubic simulation box and a
suitable aqueous environment for the bilayer I generated from crystal
data. However, since the box is cubic, there is plenty of room for
unwanted water-alkyl interaction. genbox accordingly placed water in
hydrophobic places. The water molecules should (almost) only interact
with with the lipid headgroups and water. Any helpful comment is greatly
appreciated.

You might find some useful information here:

http://wiki.gromacs.org/index.php/Membrane_Simulations

-Justin

Post by Carsten Selle
Best regards,
Carsten
--
Dr. Carsten Selle
University of Leipzig
Institute for Experimental Physics I
PWM
Linnestr. 5
D-04103 Leipzig
Germany
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | [phone]
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================

[chris.neale]

Post by Carsten Selle
Dear gromacs users,
the gel phase of some lipids as the L beta prime of DPPC is
characterized by all-trans alkyl chains which are tilted with respect to
the bilayer normal. I would like to set set up a system analog to the
one described by Venable, Brooks & Pastor, J. Chem. Phys., 112 (2000),
pp. 4822. They used a periodic box which is cubic (39 x 39 x 63 A***3).
I tried editconf and genbox to generate a cubic simulation box and a
suitable aqueous environment for the bilayer I generated from crystal
data. However, since the box is cubic, there is plenty of room for
unwanted water-alkyl interaction. genbox accordingly placed water in
hydrophobic places. The water molecules should (almost) only interact
with with the lipid headgroups and water. Any helpful comment is greatly
appreciated.
Best regards,
Carsten

Try keepbyz.sh at http://wiki.gromacs.org/index.php/Membrane_Simulations

Also note that, assuming your membrane normal is along z, editconf
will make the box bigger than you would like in the xy plane since it
probably doesn't fit perfectly by PBC and water will come in (at the
sides especially) during initial equilibration. If your gel really
does do PBC already then try just cutting down the x and y and
checking it out via g_mindist to ensure the crash is not too bad in a
trial-and-error process. You could also try inflategro from the
Tieleman lab without using a protein and that may help you get the
sides, although I am not sure that this would work as expected.

Chris.

[Marc F. Lensink]

Post by Carsten Selle
Dear gromacs users,
the gel phase of some lipids as the L beta prime of DPPC is
characterized by all-trans alkyl chains which are tilted with respect to
the bilayer normal. I would like to set set up a system analog to the
one described by Venable, Brooks & Pastor, J. Chem. Phys., 112 (2000),
pp. 4822. They used a periodic box which is cubic (39 x 39 x 63 A***3).
I tried editconf and genbox to generate a cubic simulation box and a
suitable aqueous environment for the bilayer I generated from crystal
data. However, since the box is cubic, there is plenty of room for
unwanted water-alkyl interaction. genbox accordingly placed water in
hydrophobic places. The water molecules should (almost) only interact
with with the lipid headgroups and water. Any helpful comment is greatly
appreciated.

perhaps your box is too large in the xy-direction? shorten it and try
again until it's okay. you can avoid water placement inside the
bilayer by setting a van der waals radius of 0.35 or so on those
carbons.

you can also try a different approach: i recently took an equilibrated
popc bilayer, saturated the double bond and added 2 carbons to the
sn-1 chain (the shorter one). after some equilibration the system
tightened to gel phase within 10 ns of simulation. 20 degree tilt, by
the way.

cheers,
marc

[Carsten Selle]

Post by Carsten Selle
Dear gromacs users,

Post by Carsten Selle
the gel phase of some lipids as the L beta prime of DPPC is
characterized by all-trans alkyl chains which are tilted with respect to
the bilayer normal. I would like to set set up a system analog to the
one described by Venable, Brooks & Pastor, J. Chem. Phys., 112 (2000),
pp. 4822. They used a periodic box which is cubic (39 x 39 x 63 A***3).
I tried editconf and genbox to generate a cubic simulation box and a
suitable aqueous environment for the bilayer I generated from crystal
data. However, since the box is cubic, there is plenty of room for
unwanted water-alkyl interaction. genbox accordingly placed water in
hydrophobic places. The water molecules should (almost) only interact
with with the lipid headgroups and water. Any helpful comment is greatly
appreciated.
Best regards,
Carsten

Try keepbyz.sh at http://wiki.gromacs.org/index.php/Membrane_Simulations
Also note that, assuming your membrane normal is along z, editconf
will make the box bigger than you would like in the xy plane since it
probably doesn't fit perfectly by PBC and water will come in (at the
sides especially) during initial equilibration. If your gel really
does do PBC already then try just cutting down the x and y and
checking it out via g_mindist to ensure the crash is not too bad in a
trial-and-error process. You could also try inflategro from the
Tieleman lab without using a protein and that may help you get the
sides, although I am not sure that this would work as expected.
Chris.

Dear Justin and Chris,

Thank you very much for your kind advice. I am happy to follow your
suggestions. This might be an exotic (merely nonphysiological) topic.
Thus, I try to elucidate it in the following in order to make it more
accessible for future discussions/search.

A section of the the L beta prime (gel) phase looks schematically like
"drawn" in the following, with "o" being the polar headgroups and and
"/" the hydrophobic tails.

oooooooo
////////
////////
oooooooo

The attempt to establish a (rectangular) simulation box and a solvent
environment resulted in the following, with "|" and "-" being the z and
x or y box boundaries, respectively, and "*" representing the solvent
molecules:

|----------|
|**********|
|**oooooooo|
|*////////*|
|*////////*|
|oooooooo**|
|**********|
|----------|

One observes that water really comes in at the sides, as Chris pointed
out. Apart from that, the model is close to figure 1 (left panel) in the
reference from Venable et al.(2000). As the chain contacts are very
close in gel phases in general and specifically in the crystal-derived
structure that I used, water is not introduced in interstices between
the chains. The wiki article mentioned above seems to focus on the
latter problem which is not that applicable in the case summarized here.

Best wishes, and thanks again
Carsten

[chris.neale]

Carsten, did you try what I suggested about simply reducing the x and
y by band right in your .gro (or a copy of it)? If it is truly
starting as a crystal then this should work perfectly.. did for mein
the past.

Chris

-- original message --

Dear Justin and Chris,

Thank you very much for your kind advice. I am happy to follow your
suggestions. This might be an exotic (merely nonphysiological) topic.
Thus, I try to elucidate it in the following in order to make it more
accessible for future discussions/search.

A section of the the L beta prime (gel) phase looks schematically like
"drawn" in the following, with "o" being the polar headgroups and and
"/" the hydrophobic tails.

oooooooo
////////
////////
oooooooo

The attempt to establish a (rectangular) simulation box and a solvent
environment resulted in the following, with "|" and "-" being the z and
x or y box boundaries, respectively, and "*" representing the solvent
molecules:

|----------|
|**********|
|**oooooooo|
|*////////*|
|*////////*|
|oooooooo**|
|**********|
|----------|

One observes that water really comes in at the sides, as Chris pointed
out. Apart from that, the model is close to figure 1 (left panel) in the
reference from Venable et al.(2000). As the chain contacts are very
close in gel phases in general and specifically in the crystal-derived
structure that I used, water is not introduced in interstices between
the chains. The wiki article mentioned above seems to focus on the
latter problem which is not that applicable in the case summarized here.

Best wishes, and thanks again
Carsten