[gmx-users] lipid gel phase simulation model building

[chris.neale at utoronto.ca]

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