**From:** Akshay Prabhakant (*akshayresearch16_at_gmail.com*)

**Date:** Fri Mar 22 2019 - 05:01:55 CDT

**Next message:**Giacomo Fiorin: "Re: Constraint failure in rattle algorithm for some atoms, simulation becomes unstable"**Previous message:**William Tao: "Fastest way to get PSF file for pure QM simulation?"**Next in thread:**Giacomo Fiorin: "Re: Constraint failure in rattle algorithm for some atoms, simulation becomes unstable"**Reply:**Giacomo Fiorin: "Re: Constraint failure in rattle algorithm for some atoms, simulation becomes unstable"**Reply:**Brian Radak: "Re: Constraint failure in rattle algorithm for some atoms, simulation becomes unstable"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

## 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.

**Next message:**Giacomo Fiorin: "Re: Constraint failure in rattle algorithm for some atoms, simulation becomes unstable"**Previous message:**William Tao: "Fastest way to get PSF file for pure QM simulation?"**Next in thread:**Giacomo Fiorin: "Re: Constraint failure in rattle algorithm for some atoms, simulation becomes unstable"**Reply:**Giacomo Fiorin: "Re: Constraint failure in rattle algorithm for some atoms, simulation becomes unstable"**Reply:**Brian Radak: "Re: Constraint failure in rattle algorithm for some atoms, simulation becomes unstable"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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