Hi all,
After having "hacked" the topology file of my system,
so that to have the protein (which is actually a dimer) and the ligand
belonging to the same solute molecule,
I still see them breaking up (both the two monomers and the ligand)
when the complex (i.e. solute) reaches the borders of the simulation box.
I have also post-processed the trajectory centering and imaging the
system (the solute has 95 residues) with the following commands:
trajin complex_dyn.mdcrd
center :1-95 mass origin
image origin center familiar
trajout complex_dyn.imaged.netcdf netcdf
But still the solute (complex) breaks up.
Any idea/hint about this behaviour would be really appreciated.
Thank you in advance.
Best wishes,
--
Dr Massimiliano Porrini
Institute for Condensed Matter and Complex Systems
School of Physics & Astronomy
The University of Edinburgh
James Clerk Maxwell Building
The King's Buildings
Mayfield Road
Edinburgh EH9 3JZ
Tel +44-(0)131-650-5229
E-mails : M.Porrini.ed.ac.uk
mozz76.gmail.com
maxp.iesl.forth.gr
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 30 2012 - 06:00:05 PDT
