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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Received on Wed Jul 22 2009 - 10:07:38 PDT
