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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