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

Oliver Stueker ostueker at gmail.com
Mon May 2 21:53:05 CEST 2011


I recently came across the CELLmicrocosmos 2.2 MembraneEditor, in
which one can easily generate coordinates for mixed membranes and
AFAIK also insert a protein.


I haven't had the chance/need to actually try it, though.


2011/5/2 Ioannis Beis <ibeis at mail.student.oulu.fi>:
> Hello,
> I would like to thank Justin and Tom for their kind replies to my question!
> I believe that by having the gromacs manual as a guide I would manage to
> bring the bilayer into physiological size by using Justin's advice. However,
> Tom's advice sounds simpler to implement. Unfortunately the size of the
> pre-equilibrated POPC is too small for what I want to do afterwards, but I
> can make my own POPC using editconf, genconf and Inflategro to shrink and
> equilibrate it first and then use the renaming trick.
> For beginner users that will consult this thread in the future, I had
> overestimated the value of the coordinate files as starting structures...
> Deleting the last two united atoms from oleoyl will fix the hydrocarbon
> chain length and using a palmitoyl force field will take care of turning the
> double bond into a single one. Renaming the three different united atoms'
> names in the polar heads and eventually the names of the whole lipids is
> like turning ethanolamine into choline and vice versa. The initial positions
> at the crucial points will be very improper, but this isn't important since
> hopefully the energy minimization will fix them. This strategy -with a
> little more work- could even be applied for more diverse polar heads as soon
> as one has a force field, just by placing his atoms at very reasonable
> initial positions! Proper topology file is all that matters :).
> Thanks again for your ideas!
> Yiannis

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