Dear Gromacs users,
I am trying to simulate a protein in a box of triglycerides TG (not in a
membrane)
with only a few water molecules.
I have allready build the topology file for the lipid.
to obtain this system I have run 3 simulations (with position restraints
on protein) with
triclinic box adding more TG at each run.
The lipids aggregated and surround the protein (as expected) but
asymetricaly in the box.
I have selected only the lipids from the last run
at a maximum distance of 20 A from the protein.
my problem is that my system is now circular (due to the lipid selection
method) and I want to put it in a new box
without adding more lipid or water but there will be no lipids in the
box corners.
Is there an easy way to solve this (the is no circular boxes and I have
some problems using dodecahedron ones)?
maybe it could be possible to do a very big system then
define a box with only the protein and some lipids and do not select
lipids out of this box, excluding them
(I do not know if it is clear enough )
Thanks in advance.
SEB.
--
_______________________________________________________
Sébastien SANTINI, PhD
http://sebastien.santini.free.fr
CBMN, Faculté Universitaire des Sciences Agronomiques
Passage des déportés, 2
B-5030 Gembloux, BELGIQUE
GSM: 00 32 (0)4 98 59 53 65
_______________________________________________________
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