From: Akshay Prabhakant (akshayresearch16_at_gmail.com)
Date: Fri Mar 22 2019 - 05:01:55 CDT
## OUTPUT/INPUT
# Amber/(t,s,x)leap generated parm and crd file
parmfile apo_cap.prmtop
# Input
set temperature 300
ambercoor apo_cap.rst7
## bin coord ##
bincoordinates min_02.restart.coor
#binvelocities min_02.restart.vel
extendedSystem min_02.restart.xsc
# Output
restartfreq 1
dcdfreq 1
xstFreq 1
outputEnergies 1
outputPressure 1
outputname eq_01
## SIMULATION PARAMETERS
# AMBER FF settings
amber on
rigidBonds all
useSettle on
rigidTolerance 1.0e-8
cutoff 10.0
pairlistdist 11.0
switching off
exclude scaled1-4
readexclusions yes
1-4scaling 0.83333333
scnb 2.0
zeromomentum on
ljcorrection on
watermodel tip3
# Integrator Parameters
timestep 1.00
nonbondedFreq 1
fullElectFrequency 1
stepspercycle 1
# PME settings
PME on
PMETolerance 1.0e-6
PMEInterpOrder 4
FFTWUseWisdom no
PMEGridSizeX 54
PMEGridSizeY 54
wrapAll on
PMEGridSizeZ 54
## position restraints ##
constraints on
consref modified_cap.pdb
conskfile modified_cap.pdb
conskcol B
constraintScaling 10.0
### NVT ###
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# periodic cell
cellBasisVector1 50.8726134 0.0 0.0
cellBasisVector2 0.0 50.8903175 0.0
cellBasisVector3 0.0 0.0 50.8639184
cellOrigin 0.0 0.0 0.0
binaryoutput yes
binaryrestart yes
## EXECUTION SCRIPT
temperature 0
seed 1010 # Initial velocity distribution is performed to meet this Initial
temperature (in K)
reassignFreq 1 # Number of steps between reassignment of velocities (e)
reassignIncr 0.01 # Increment used to adjust temperature during temperature
reassignment
reassignTemp $temperature # The value of temperature to be kept after
heating is completed
reassignHold $temperature
numsteps 100
This is the equilibration script that i use for raising temperature of my
system from 0 to 300K. It seems to be giving the following error:
REASSIGNING VELOCITIES AT STEP 0 TO 300 KELVIN.
ERROR: Constraint failure in RATTLE algorithm for atom 4043!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 49!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 2919!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 3188!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 214!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 5045!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 6347!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 4843!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 2268!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 3314!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 3329!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 3627!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 4925!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
Can somebody help me in fixing this, I have tried to minimize my structure
for a very long time too, but I still get this error. Is anything wrong
with my script? If so, please mention the corrections. Thanks in advance.
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