From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Tue Jul 05 2011 - 10:13:57 CDT
Hi all
I am trying to run a md simulation of a membrane protein imbedded in a
membrane - I have followed the tutorial on membrane proteins but when
I try to apply for an example a equilibration run with the lipid tail
freezing water, protein, and head group I get the following error
ERROR: Constraint failure in RATTLE algorithm for atom 44585!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 44884!
ERROR: Constraint failure; simulation has become unstable.
I have minimized the whole system with a gradient of
LINE MINIMIZER REDUCING GRADIENT FROM 39.3483 TO 0.0393483
but as soon as velocities are assigned to the system(the protein and
water is still frozen setting the b-factor to 1) I get the following
error as stated above. My step size is 2 fs using SHAKE and I am using
the following for electrostatics
#PME (for full-system periodic electrostatics)
PME yes
# let NAMD determine grid
PMEGridSpacing 1.0
and the following extra parameters for the pressure
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigid bonds
useFlexibleCell yes ;# no for water box, yes for membrane
useConstantArea no ;#
I have tried to change the useConstantArea but same problem.
How to resolve the problem thanks in advance
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