Re: membrane simulation ERROR rattle algorithm

From: sajad falsafi (sajad.falsafi_at_yahoo.com)
Date: Tue Jul 05 2011 - 11:44:10 CDT

Hi

How many n-steps of minimization do you have in your conf file? We guess that
your n-steps of minimize is low.

You can increase number of steps inminimize option. after this if you have
problem, you cansaving a trajectory file at every step and looking at it in VMD,
this should show clearly which atoms are being affected. Fix this, and try
minimizing with more steps.

Hope this helps you
Sajad & Zahra

________________________________
From: Jorgen Simonsen <jorgen589_at_gmail.com>
To: namd-l_at_ks.uiuc.edu
Sent: Tue, July 5, 2011 7:43:57 PM
Subject: namd-l: membrane simulation ERROR rattle algorithm

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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