[gmx-users] lipid solvent

sebastien santini 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 
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.



 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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