Hi,
Thanks for ur reply... u mean do i need to just re run all the
simulations once more?
Rajesh
On Wed, 06 Jul 2011 18:03:26 +0200
Adrian Roitberg <roitberg.qtp.ufl.edu> wrote:
> 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
>> /
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> 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 - 09:30:06 PDT
