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.
Kindest regards,
Yiannis
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