[gmx-users] How to use Inflategro with different lipid types

Ioannis Beis ibeis at mail.student.oulu.fi
Sun May 1 07:51:19 CEST 2011

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

Kindest regards,

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