From: Cesar Luis Avila (
Date: Tue Nov 11 2008 - 18:44:07 CST

Membrane builder uses a patch of preequilibrated lipids and replicates
that patch. Just take a look at the code.

Edward Lyman escribió:
> that would be nice for starting from scratch, but if you already have
> a patch of membrane which is equilibrated (and not doing any funny
> phase separation type stuff) then i think it's faster (in terms of cpu
> expenditure) to replicate the equilibrated patch. i don't know the
> inner workings of membrane builder, but i bet it builds a bunch of
> lipids with perfectly ordered tails, and then you have to wait for the
> tails to relax into the entangled, liquid disordered phase. and that
> takes a lot of simulation.
> On Tue, Nov 11, 2008 at 12:23 PM, Cesar Luis Avila
> < <>> wrote:
> Or perhaps you would like to adapt the membrane builder tool in
> order to deal with your membrane. In that way you will be able to
> obtain a membrane of any size.
> Peter Freddolino escribió:
> Autopsf should take care of the split/recombine process
> automatically, although you'll want to verify that the results
> are reasonable. You can get at it via the command line or GUI
> (under Modeling).
> Best,
> Peter
> Edward Lyman wrote:
> Dear all,
> I have a pdb and a psf for a membrane system, and I want
> to build a system that is twice as big, by shifting the
> coordinates by the box dimension in y. shifting the
> coordinates and writing them to a pdb is simple enough,
> but I am trying to find a simple way to generate a
> combined pdb/psf for the whole, doubled system. if i try
> to read the psf and the first pdb, then re-read the psf
> and read the second pdb, I get an error "Unable to add
> (duplicate?) residue C001:1". but, even if I am able to do
> so, I think I might have too many residues per segment.
> In the past, I dealt with this by painstakingly splitting
> the pdb's into separate segments, renaming segments until
> I had enough, regenerating the psf's, and then sticking it
> all back together with a series of readpsf/readpdb's, then
> writing everything. But I think there must be a cleaner,
> faster, less annoying way...
> Thx,
> E