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From: Rahul Nori (rahulnori_at_gmail.com)
Date: Mon Jan 07 2013 - 12:24:25 CST

I figured out the problem. Please ignore my previous message.
Had problem with the coordinates. 

--
Thanks,
Rahul
On Mon, Jan 7, 2013 at 12:00 PM, Rahul Nori <rahulnori_at_gmail.com> wrote:
> Hi,
>
> I am running a minimization of a protein (crambin) in water sphere.
> I am getting the following error when I run the configuration file.
>
> ERROR: Constraint failure in RATTLE algorithm for atom 103!
> ERROR: Constraint failure; simulation has become unstable.
>
> This is the configuration file I am using, that I adapted from the
> tutorials:
>
> # Minimization and Equilibration of
> # Crambin in a Water Sphere
>
> structure          /Users/wser/Desktop/crambin_run/ab1_ws.psf
> coordinates        /Users/wser/Desktop/crambin_run/ab1_ws.pdb
>
> set temperature    310
> set outputname     ab1_ws_eq
>
> firsttimestep      0
>
> # Input
> paraTypeCharmm    on
> parameters
>  /Users/wser/Desktop/crambin_run/par_all27_prot_lipid.inp
> temperature         $temperature
>
>
> # Force-Field Parameters
> exclude             scaled1-4
> 1-4scaling          1.0
> cutoff              12.0
> switching           on
> switchdist          10.0
> pairlistdist        14.0
>
>
> # Integrator Parameters
> timestep            2.0  ;# 2fs/step
> rigidBonds          all  ;# needed for 2fs steps
> nonbondedFreq       1
> fullElectFrequency  2
> stepspercycle       10
>
>
> # Constant Temperature Control
> langevin            on    ;# do langevin dynamics
> langevinDamping     1     ;# damping coefficient (gamma) of 1/ps
> langevinTemp        $temperature
> langevinHydrogen    off    ;# don't couple langevin bath to hydrogens
>
> # Output
> outputName          $outputname
>
> restartfreq         500     ;# 500steps = every 1ps
> dcdfreq             250
> outputEnergies      100
> outputPressure      100
>
> # Spherical boundary conditions
> sphericalBC         on
> sphericalBCcenter   30.3081743413, 28.8049907121, 15.353994423
> sphericalBCr1       26.0
> sphericalBCk1       10
> sphericalBCexp1     2
>
> # Minimization
> minimize            100
> reinitvels          $temperature
>
> run 2500 ;# 1ps
>
>
>
> --
> Thanks,
> Rahul
>
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