Ioannis Beis wrote:
Dear gromacs users,
I am a new user of gromacs. I am currently trying to build a large
bilayer with 3 different lipid species (11 DPPC : 7 POPC : 7 POPE) and
no protein embedded in it. I have used single lipids from
pre-equilibrated bilayers available at Mr. Tieleman's website. The
distance of center of mass of neighboring lipids is 1 nm, so there are
small areas with overlaps. I was hoping that I would be able to inflate
my membrane and have the lipids totally free of overlaps using
Inflategro. Subsequently, I was planning to use the shrinking steps to
bring the membrane into physiological size. Is this strategy valid in
the first place? If not, I kindly ask for an alternative.
In case this method can be used, despite "To identify the lipid species
their actual residue name must be given" which is mentioned in the
methodology, the form "INFLATEGRO bilayer.gro scaling_factor
lipid_residue_name cutoff inflated_bilayer.gro gridsize areaperlipid.dat
(protein)" only allows the use of one lipid type. How is it possible to
run perl with all lipid types at once? I have tried performing
inflations using one lipid type at a time and they work. [It worths
mentioning that the coordinates of the rest two (uninflated) lipid types
slightly change without equilibration (I assume this has to do with
Inflategro trying to force the molecules avoid overlaps)]. But I can't
treat my membrane as a system that way. I have read the publication
introducing the methodology, but it didn't help me solve my problem.
I would be grateful if someone could help, also taking into account that
I am
inexperienced.
If you want to use InflateGRO, then you'll have to modify the code to do so. It
handles only one lipid type.
The alternative is to use "normal" MD simulations to pack the membrane. On such
approach (just thinking out loud here, so it may not work) might be to simulate
your membrane (maybe without water) with some external pressure applied to the
x-y plane to compress the lipids together. You may need position restraints on,
i.e., the lipid headgroups in the z-dimension only during this procedure so the
lipids do not simply slam into one another and distort the membrane. Once
you've achieved a reasonable membrane, solvate and equilibrate for a longer
period of time in the presence of solvent and absence of any restraints.
-Justin
Kindest regards,
Yiannis
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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