Hi
all interesting questions but in order to answer them yourself you need
a DIFFERENT set of simulations.
You need to run with the SAME set of input parameters more than once.
That will tell you how much does the rmsd vs time plots change simply
because you started the simulation with different velocities
That is the only way to ask if the plots you show are truly different
statistically or not.
Adrian
On 7/6/11 5:59 PM, Rajesh Raju wrote:
> Dear Amber users,
>
> I am working on DNA-protein interactions. I have followed the following
> steps:
>
> [1] Minimization of water box and counter ions keeping DNA and protein
> fixed with a restrained force of 500kcal/mol
> [2] Complete minimization of the whole system
> [3] Heated the system from 0 to 100 K in 100ps, then from 100 to 200 in
> 100ps and in the last stage from 200 to 300 in 100ps. So overall time is
> 300ps for the heating stage. Some of the simulations I used 1fs time
> steps, and some of them i used 1fs.
> 4] Equilibration in 3 steps
> First step: Equilibrated the system at constant pressure for 100ps with
> a restraint force of 10 kcal mol-1 on the protein and DNA.
> Second step: Equilibrated the system at constant pressure for 100ps with
> a restraint force of 1 kcal mol-1 on the protein and DNA.
> third step: Free equilibration without any constraints. some of the
> simulations I performed 1ns equilibration, some of them I performed 2ns.
> Also I used time steps 1 fs and 2fs for some of the simulations.
> [5] production stage simulation for 4ns. Except for one simulation (C)
> all other simulations are in NVT ensemble. For prodution stage
> simulations I used only 2fs time steps.
>
> I have performed 9 (A-I) different simulations with different
> temperature coupling parameter (gamma_ln ) and pressure couling
> parameters (taup).
>
> For simulation A: gamma_ln=2, taup=2, dt=1 fs for heating and
> equilbration, Equilibration stage3 1ns
> For simulation B: gamma_ln=3, taup=3, dt=1 fs for heating and
> equilbration, Equilibration stage3 1ns
> For simulation C: gamma_ln=2, taup=2, dt=1 fs for heating and
> equilbration, Equilibration stage3 1ns, production ensemble NPT
> For simulation D: gamma_ln=2, taup=5, dt=1 fs for heating and
> equilbration, Equilibration stage3 1ns
> For simulation E: gamma_ln=2, taup=1, dt=2 fs for heating and
> equilbration, Equilibration stage3 1ns
> For simulation F: gamma_ln=3, taup=3, dt=2 fs for heating and
> equilbration, Equilibration stage3 1ns
> For simulation G: gamma_ln=1, taup=1, dt=2 fs for heating and
> equilbration, Equilibration stage3 1ns
> For simulation H: gamma_ln=1, taup=1, dt=2 fs for heating and
> equilbration, Equilibration stage3 2ns
> For simulation I: gamma_ln=2, taup=2, dt=2 fs for heating and
> equilbration, Equilibration stage3 2ns
>
> Notes: B and F differs only in the time step(dt), G and H differs in the
> equlibration stage3 length
>
>
>
>
>
> I calculated the RMSD deviations withrest to the first frame (BLACK
> lines in the RMSD plots) in the production stage and also with repect to
> the minimized structure after minimzation step2 (RED lines).. I have
> attached the RMSD plots. The RMSD plots shows a large variation upon
> changing the simulation parameters..?
>
> My questions:
>
> If these trajectories differ by changing the simulations parameters, how
> we can trust these results?
> Is there any 'best parameters for gamma_ln and taup.
> Is there any problems in the MD protocol which I followed?
> What is the reason for the odd behaviour in the RMSD plots and what
> should I do to get a stable MD trajectory?
>
>
>
> This is the sample inputfile I used for the simulation A:
> My inputs: I just changed the respective parameters (gamma, taup, dt,
> simulation lenghth) in the input files
>
> Min1:
>
> Minimization solvent + ions Stage 1
> &cntrl
> imin = 1,
> maxcyc = 10000,
> ncyc = 5000,
> ntb = 1,
> ntr = 1,
> cut = 12.0
> /
> Hold the Solute fixed
> 500.0
> RES 1 437
> END
> END
>
> Min2.in
>
>
> Minimization whole system
> &cntrl
> imin = 1,
> maxcyc = 10000,
> ncyc = 5000,
> ntb = 1,
> ntr = 0,
> cut = 12.0
> /
>
>
> Heat1:
>
> Heating Stage 1
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 1,
> cut = 12.0,
> ntr = 1,
> ntc = 2,
> ntf = 2,
> tempi = 0.0,
> temp0 = 100.0,
> ntt = 3,
> gamma_ln = 2.0,
> nstlim = 100000, dt = 0.001
> ntpr = 1000, ntwx = 1000, ntwr = 1000
> /
> weak restraints on solute
> 10.0
> RES 1 437
> END
> END
>
>
> Heat2:
> Heating Stage 2
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 1,
> cut = 12.0,
> ntr = 1,
> ntc = 2,
> ntf = 2,
> tempi = 100.0,
> temp0 = 200.0,
> ntt = 3,
> ig = -1,
> gamma_ln = 2.0,
> nstlim = 100000, dt = 0.001
> ntpr = 1000, ntwx = 1000, ntwr = 1000
> /
> weak restraints on solute
> 10.0
> RES 1 437
> END
> END
>
>
> Heating Stage 3
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 1,
> cut = 12.0,
> ntr = 1,
> ntc = 2,
> ntf = 2,
> tempi = 200.0,
> temp0 = 300.0,
> ntt = 3,
> ig = -1,
> gamma_ln = 2.0,
> nstlim = 100000, dt = 0.001
> ntpr = 1000, ntwx = 1000, ntwr = 1000
> /
> weak restraints on solute
> 10.0
> RES 1 437
> END
> END
>
> Equilibration Stage 1
> &cntrl
> imin=0,irest=1,ntx=5,
> ntc=2,ntf=2,
> cut=12.0,
> ntb=2, ntp=1, taup=2.0,
> ntt=3, gamma_ln=2.0, ig=-1,
> temp0=300.0,
> tempi=300.0,
> ntr=1,
> nstlim=100000,dt=0.001,
> ntpr=1000, ntwx=1000, ntwr=1000
> /
> weak restraints on solute
> 10.0
> RES 1 437
> END
> END
>
>
> Equilibration Stage 2
> &cntrl
> imin=0,irest=1,ntx=5,
> ntc=2,ntf=2,
> cut=12.0,
> ntb=2, ntp=1, taup=2.0,
> ntt=3, gamma_ln=2.0, ig=-1,
> temp0=300.0,
> tempi=300.0,
> ntr=1,
> nstlim=100000,dt=0.001,
> ntpr=1000, ntwx=1000, ntwr=1000
> /
> weak restraints on solute
> 1.0
> RES 1 437
> END
> END
>
> Equilibration Stage 3
> &cntrl
> imin=0,irest=1,ntx=5,
> ntc=2,ntf=2,
> cut=12.0,
> ntb=2, ntp=1, taup=2.0,
> ntt=3, gamma_ln=2.0, ig=-1,
> temp0=300.0,
> tempi=300.0,
> nstlim=1000000,dt=0.001,
> ntpr=1000, ntwx=1000, ntwr=1000
> /
>
>
> MD Production Stage
> &cntrl
> imin = 0,
> irest = 1,
> ntx = 5,
> ntb = 1,
> cut = 12.0,
> ntc = 2,
> ntf = 2,
> temp0 = 300.0,
> tempi = 300.0,
> ntt = 3,
> ig = -1,
> gamma_ln = 2.0,
> nstlim = 2000000, dt = 0.002
> ntpr = 1000, ntwx = 1000, ntwr = 1000
> /
>
>
>
> _______________________________________________
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--
Dr. Adrian E. Roitberg
Full Professor
Quantum Theory Project, Department of Chemistry
University of Florida
on Sabbatical in Barcelona until August 2011.
Email roitberg.ufl.edu
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Received on Wed Jul 06 2011 - 09:30:04 PDT
