From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Mar 22 2019 - 08:08:24 CDT
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
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