**From:** Giacomo Fiorin (*giacomo.fiorin_at_gmail.com*)

**Date:** Fri Mar 22 2019 - 08:08:24 CDT

**Next message:**Brian Radak: "Re: Constraint failure in rattle algorithm for some atoms, simulation becomes unstable"**Previous message:**Akshay Prabhakant: "Constraint failure in rattle algorithm for some atoms, simulation becomes unstable"**In reply to:**Akshay Prabhakant: "Constraint failure in rattle algorithm for some atoms, simulation becomes unstable"**Next in thread:**Brian Radak: "Re: Constraint failure in rattle algorithm for some atoms, simulation becomes unstable"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi Akshay, the trouble with minimization is that it will bring the system

to the closest *local* minimum, which may very well be located right atop a

1000 kcal/mol energy beak.

The standard way is visualizing your initial structure in VMD and checking

those atom numbers up. You can also load the final minimized structure as

a new frame. If there is a poor geometry, that will require going back to

the setup phase to correct the problem.

Giacomo

On Fri, Mar 22, 2019 at 6:03 AM Akshay Prabhakant <

akshayresearch16_at_gmail.com> wrote:

*> ## 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.
*

*>
*

-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin

**Next message:**Brian Radak: "Re: Constraint failure in rattle algorithm for some atoms, simulation becomes unstable"**Previous message:**Akshay Prabhakant: "Constraint failure in rattle algorithm for some atoms, simulation becomes unstable"**In reply to:**Akshay Prabhakant: "Constraint failure in rattle algorithm for some atoms, simulation becomes unstable"**Next in thread:**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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