COntraints for lipid bilayer simulation

From: priti arora (priti0806_at_gmail.com)
Date: Tue Apr 24 2007 - 05:56:12 CDT

Hi

I am working on the simulation of POPC lipid bilayer. The membrane was
generated by VMD plugin only but it has unacceptable bond order when checked
by VEGA ZZ software. The simulation worked well in its minimisation step but
in the equilibrium step it stopped showing the error messages:

###################

ERROR: Constraint failure in RATTLE algorithm for atom 16666!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 30304!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 30559!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 41302!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 41838!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 26269!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 26538!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 27746!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 37818!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely.
###################

 I am not using any constraints as am not sure which constraints are to be
used in case of lipids. What are the constraints required for lipid and for
lipid and protein together.

Thanks and regards,

Priti Arora
MSc in Drug Delivery
School of Pharmacy
University of London
Tel: +44 7983024922 (Mob)
       +44 2072895561 (Hm)
       +44 2077535923 (Lab)

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