From: Marcelo Puiatti (marcelo.puiatti_at_gmail.com)
Date: Wed Apr 11 2007 - 09:46:38 CDT
Dear users:
I'm trying to run a NTV equilibration. But I allways find the same message.
ERROR: Constraint failure in RATTLE algorithm for atom nnnn!
I tried to find the solution to my problem in the list, I found a lot off
scenarios where the same problem appears and in VERY DIFFERENT condittions.
However, it seems there are to possible solutions (according to the list):
Modiffing the PME grid size
Relaxing the structure more steps
Which is the best solution?
Is this problem directly related with my structure?
I work with the same structure with AMBER and it does work nicelly
Is there any cuttoff in the Gradient that make things don't work?
Thanks in advance
Marcelo
P.D. The protein contains 1120 residues and aprox. 28200 solvent molecules
I attached the config file:
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
set temperature 300
set outputname NTV
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm off
paratypeXplor off
amber on
parmfile myprotein.top
ambercoor myprotein.restrt
# parameters ../common/par_all27_prot_lipid.inp
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 0.833333 # =1/1.2, default is 1.0
cutoff 11.5
switching on
switchdist 9.
pairlistdist 13.5
# Integrator Parameters
timestep 1.5 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
cellBasisVector1 88.15 0. 0.
cellBasisVector2 0. 88.72 0.
cellBasisVector3 0. 0.0 153.14
cellOrigin 45.52 45.94 78.17
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 128
PMEGridSizeY 128
PMEGridSizeZ 194
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
#Constraints
constraints on
consexp 6
consRef myproteinConst.pdb
consKFile myproteinConst.pdb
consKCol B
# Output
outputName $outputname
restartfreq 200 ;# 500steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 50
outputPressure 50
#############################################################
## EXTRA PARAMETERS ##
#############################################################
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
# minimize 2000
reinitvels $temperature
run 50000
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:34 CST