AMBER Archive (2009)

Subject: Re: [AMBER] Equilibration step

From: Tom Joseph (ttjoseph_at_gmail.com)
Date: Wed Jul 22 2009 - 07:35:15 CDT

Where did you get your protein and how did you prepare it for
simulation? Did you minimize your structure (imin=1) before heating?

--Tom

On Wed, Jul 22, 2009 at 5:47 AM, Olotu Odunayo<paxoo_at_nottingham.ac.uk> wrote:
> Hi,
>
> I am new to molecular simulation, and I am having problems going past the equilibration stage.
>
> After equilibration, when I view the average pdb structure, it doesn't look right.
> 1, RMSD is around 2.75 to 3
> 2, Some water molecules are skewed together (like having bonds overstretched during minimisation etc)
>
> I have tried heat up with restraints, then equilibrating without restraints - some residues of my protein were distorted and I get MPI Quiescence error when i try to do production run
>
> I have tried equilibration with restraints and gradually reducing restraints, the pdb actually looks fine but there is large RMSD and bonds in water molecule overstretched.
>
> Please can you help, below is a typical input file
>
> Heat up
> 20ps MD with res on protein
>  &cntrl
>  imin   = 0,
>  irest  = 0,
>  ntx    = 1,
>  ntb    = 1,
>  cut    = 10,
>  ntr    = 1,
>  ntc    = 2,
>  ntf    = 2,
>  tempi  = 0.0,
>  temp0  = 300.0,
>  ntt    = 3,
>  gamma_ln = 1.0,
>  nstlim = 10000, dt = 0.002,
>  ntpr = 250, ntwx = 250, ntwr = 10000
>  /
> Keep protein fixed with weak restraints
> 10.0
> RES 1 270
> END
> END
>
> Equilibration
>
> Equilibrate density
>  &cntrl
>   imin=0, irest=1, ntx=5,
>   ntb=2, ntp=1, cut=10.0,
>   ntf=2, ntc=2,
>   nstlim=100000, dt=0.002,
>   ntpr=500, ntwx=500,
>   ntr=0,
>   ntt=3, gamma_ln=1., temp0=300.0,
>  /
>
> I also tried
>
> Heat up to 100
> Warm it up restraining Protein water and ions free
>  &cntrl
>   imin=0, irest=0, ntx=1,
>   ntb=1, cut=10.0,
>   ntf=2, ntc=2,
>   nstlim=10000, dt=0.002,
>   ntpr=100, ntwx=200,
>   ntr=1,
>   ntt=3, gamma_ln=1., temp0=100.0, tempi=0.0,
>  /
> Hold Protein fixed
> 100.0
> RES 1 270
> END
> END
>
> Heat to 300
>  MD on water and ions around free raising T to 300K
>  &cntrl
>        nmropt=1,
>        imin=0, irest=1, ntx=5,
>        ntf=2, ntb=2, cut=10.0,
>        ntr=1,
>        nstlim=10000, dt=0.002,
>        ntpr=100, ntwx=200,
>        ntt=3, gamma_ln=1, temp0=300.0, tempi=100.0,
>        ntp=1,
>        ntc=2,
>  &end
>  &wt
>        type='TEMP0', istep1=0, istep2=9999, value1=100.0, value2=300.0
>  &end
>  &wt
>        type='END'
>  &end
> Hold Protein Fixed
> 100.0
> RES 1 270
> END
> END
>
> Equilibration step reducing restraint by half
> &cntrl
>   imin=0, irest=1, ntx=5,
>   ntb=2, cut=10.0,
>   ntf=2, ntc=2,
>   nstlim=10000, dt=0.002,
>   ntpr=100, ntwx=200,
>   ntr=1, ntp=1,
>   ntt=3, gamma_ln=1., temp0=300.0,
>  /
> Hold Protein fixed
> 50.0
> RES 1 270
> END
> END
>
> I reduced to 25.0, 10.0, 5.0, 1.0, then no restraint
>
> Thanks
>
>
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