From: Anton Arkhipov (anton_at_ks.uiuc.edu)
Date: Mon Dec 07 2009 - 10:15:53 CST

Francesco,

Since you eventually want to work with POPC, maybe just go ahead and
work with that, and skip DOPC?

> I could build
> the cg POPC bilayer from my non equilibrated bilayer (I just made a
> 80x80 membrane with Balabin plugin). Probably, however, equilibration
> should be first carried out all-atoms.
No, the membrane that VMD membrane builder gives you is already
decently equilibrated, so don't worry about it. That membrane patch
should be good to go.

As you mentioned, one can also use equilibrated membranes from the
CHARMM-GUI web site. But for POPC, what VMD gives you is sufficient.

Anton.

On Dec 6, 2009, at 11:24 AM, Francesco Pietra wrote:

> Hi Anton:
> Thanks for completing the panorama. As you provided bead definitions
> for both DOPC (dopc.cgc) and POPC (lipid.cgc), do you have also
> dopc.psf? I extracted the single dopc molecule pdb from Feller's
> equilibrated dopc bilayer but AutoPSF requests parameters, indicating
> that the missing ones can be obtained with Paratool (which I have
> never used yet). In my hands, the CG Builder does not work without
> both psf and pdb,
>
> For POPC (which for final work I would prefer to DOPC) I have both pdb
> and psf but no equilibrated bilayer found on the web. I could build
> the cg POPC bilayer from my non equilibrated bilayer (I just made a
> 80x80 membrane with Balabin plugin). Probably, however, equilibration
> should be first carried out all-atoms.
>
> thanks
> francesco
>
> On Sun, Dec 6, 2009 at 7:35 AM, Anton Arkhipov <anton_at_ks.uiuc.edu>
> wrote:
>> Hi Francesco,
>>
>> Just to add to whatever help you got already:
>>
>> for an rbcg bilayer, take an equilibrated all-atom bilayer, and
>> convert it
>> to rbcg. If you want to be extra careful, then you can solvate the
>> result
>> with rbcg water and use rbcg simulation to equilibrate the bilayer
>> further.
>>
>> For sbcg, there's no direct conversion available, but it's not
>> necessary,
>> because the model is extremely simple - just two beads connected by
>> a spring
>> make one "molecule", and a bunch of such molecules constitute a
>> leaflet. So
>> if you need an sbcg bilayer, it's very simple to just create a pdb
>> with such
>> molecules by hand. You cna put those sbcg "molecules" uniformly
>> distributed
>> in the bilayer, and then equilibrate them with sbcg simulations.
>>
>> Anton.
>>
>>
>> On Dec 2, 2009, at 10:13 AM, Francesco Pietra wrote:
>>
>>> Hi;
>>> After I posted the subject problem as secondary matter, I carried
>>> out
>>> an accurate search on the web, unable to find an equilibrated rbcg
>>> lipid bilayer for vmd 1.8.7/namd martini implementation (or a plain
>>> procedure to get it from scratch). As for sbcg, I guess that direct
>>> conversion from an equilibrated all-atoms lipid bilayer will not
>>> work.
>>> Thanks for info.
>>> francesco pietra
>>
>>