RATTLE error with lipid bilayer system

From: Ahmad Kiani Karanji (ahmadkiani2014_at_gmail.com)
Date: Tue Nov 21 2017 - 13:08:46 CST

Hello NAMD users

I'm running POPC-POPG lipid bilayer system with hexamer blue
proteorhodopsin inside it. I'm following the Charmm-gui input files. The
raw files are working fine but I modified the system. I added some lipids
in the middle of the protein and also retinal (resname RET is connected to
the Lys 213) to the protein.
 My plan was to start with minimization and then going for equilibration
but when the minimization finished my simulation crashed. It didn't even
start equilibration.

The error that I got is:
ERROR: Constraint failure in RATTLE algorithm for atom 73327!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
(atom 73327 is in lipid part of the system.)

I also have this warning when I'm minimizing my structure:
Warning: Bad global dihedral count!
Warning: Bad global improper count!

When I comment out the restraints (including planar restraint and dihedral
restraint) simulation goes well, otherwise I get error.
I running the system with 1fs timestep. I have no control on boundaries
because charmm-gui define them by a formula. Different numbers of lipids
doesn't work also. I tried to increase minimization steps, this one doesn't
work also.
I think this problem doesn't have anything to do with my protein because I
ran it with detergents successfully.
It would be appreciated if someone give a suggestion to overcome this error.


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