[gmx-users] lipid solvent
santini.s at fsagx.ac.be
Tue May 15 15:12:32 CEST 2007
Dear Gromacs users,
I am trying to simulate a protein in a box of triglycerides TG (not in a
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
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.
Sébastien SANTINI, PhD
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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