Tutorial-l Mailing List

From: Rahul Nori (rahulnori_at_gmail.com)
Date: Mon Jan 07 2013 - 12:00:47 CST

Hi,

I am running a minimization of a protein (crambin) in water sphere.
I am getting the following error when I run the configuration file.

ERROR: Constraint failure in RATTLE algorithm for atom 103!
ERROR: Constraint failure; simulation has become unstable.

This is the configuration file I am using, that I adapted from the
tutorials:

# Minimization and Equilibration of
# Crambin in a Water Sphere

structure /Users/wser/Desktop/crambin_run/ab1_ws.psf
coordinates /Users/wser/Desktop/crambin_run/ab1_ws.pdb

set temperature 310
set outputname ab1_ws_eq

firsttimestep 0

# Input
paraTypeCharmm on
parameters
 /Users/wser/Desktop/crambin_run/par_all27_prot_lipid.inp
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Output
outputName $outputname

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
outputEnergies 100
outputPressure 100

# Spherical boundary conditions
sphericalBC on
sphericalBCcenter 30.3081743413, 28.8049907121, 15.353994423
sphericalBCr1 26.0
sphericalBCk1 10
sphericalBCexp1 2

# Minimization
minimize 100
reinitvels $temperature

run 2500 ;# 1ps 

--
Thanks,
Rahul
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