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

[Thomas Piggot]

Hi,

To construct the bilayer I would just take an equilibrated POPC bilayer 
and then randomly pick lipids to change to POPE (just by a simple 
renaming of these lipids and the atom names in the headgroup) and DPPC 
(which would just require deletion of two united-atoms from the sn-2 
chains and renaming of the lipids). Then just run for an equilibration 
on the bilayer to allow the changes to take effect.

There are other approaches you could take but I see this as the simplest 
solution.

Cheers

Tom

Justin A. Lemkul wrote:
> 
> 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
>>
> 

-- 
Dr Thomas Piggot
University of Southampton, UK.