AMBER Archive (2009)

Subject: [AMBER] Equilibration step

From: Olotu Odunayo (paxoo_at_nottingham.ac.uk)
Date: Wed Jul 22 2009 - 04:47:37 CDT

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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