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

[Justin A. Lemkul]

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
> 

-- 
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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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