I have checked AMBER14 manual to find that it is proper to use ff14SB which
is a continuing evolution of the ff99SB force field.
I am really thankful for your help prof.Jason !
Best Regards
the following protocol
> >
> > 1- 800 steps of minimization round 1 with restrains
> > &cntrl
> > imin=1, nmropt=0,
> > ntx=1, irest=0,
> > ntxo=1, ntpr=100, ntrx=1, ntwr=100, ntwx=100,
> > ntf=2, ntb=1, igb=0, ntc=2, cut=10.0,
> > maxcyc=800, ncyc=100, ntmin=1,
> > nscm=2, nrespa=1, dt=0.001,
> > ibelly=0, ntr=1, restraint_wt=5.0, restraintmask=':1-175',
> > &end
>
> >
> > 2- heating up to 100 K
> > &cntrl
> > imin=0, nmropt=0,
> > ntx=1, irest=0,
> > ntxo=1, ntpr=100, ntrx=1, ntwr=100, ntwx=100,
> > ntf=2, ntb=2, igb=0, ntc=2, cut=10.0,
> > nstlim=50000, nscm=500, nrespa=1, dt=0.001,
> > Tempi=0.0, Temp0=100.0, ntt=3, tautp=0.5, gamma_ln=2.0,
> > pres0=1.0, ntp=1, taup=1.0,
> > ntr=1, restraint_wt=5.0, restraintmask=':1-175',
> > &end
>
> >
> > 3- 800 steps of minimization round 2 without restrains
> > &cntrl
> > imin=1, nmropt=0,
> > ntx=1, irest=0,
> > ntxo=1, ntpr=100, ntrx=1, ntwr=100, ntwx=100,
> > ntf=2, ntb=1, igb=0, ntc=2, cut=10.0,
> > maxcyc=800, ncyc=100, ntmin=1,
> > nscm=500, nrespa=1, dt=0.001,
> > &end
> >
>
> > 4- heating up to 310 (over 9 rounds each of 50 ps and heating upto 25 K
> > except the last step) with restrains
> > &cntrl
> > imin=0, nmropt=0,
> > ntx=1, irest=0,
> > ntxo=1, ntpr=100, ntrx=1, ntwr=100, ntwx=100,
> > ntf=2, ntb=2, igb=0, ntc=2, cut=10.0,
> > nstlim=50000, nscm=500, nrespa=1, dt=0.001,
> > Tempi=100.0 , Temp0=125.0 , ntt=3, tautp=0.01, gamma_ln=2,
> > pres0=1.0, ntp=1, taup=0.05,
> > ntr=1, restraint_wt=5.0, restraintmask=':1-175',
> > &end
>
> > 5- production MD
> > &cntrl
> > imin=0, nmropt=0,
> > ntx=5, irest=1, ntrx=1,
> > ntxo=1, ntpr=500, ntwr=500, iwrap=1, ntwx=500,
> > ntf=2, ntb=2, igb=0, ntc=2, cut=10.0,
> > nstlim=50000, nscm=500, nrespa=1, dt=0.002,
> > Tempi=310.0, Temp0=310.0, ntt=3, tautp=0.5, gamma_ln=2,
> > pres0=1.0, ntp=1, taup=2.0,
> > &end
> >
On Thu, Feb 5, 2015 at 9:33 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> > On Feb 5, 2015, at 1:44 PM, Hadeer ELHabashy <hadeer.elhabashi.gmail.com>
> wrote:
> >
> > Dear sir
> >
> > wish you are fine !
> > Thanks for your response !
> > Actually, I used to write the control files like this because it is
> similar
> > to that printed in the output file of AMBER. However I've tried to
> simplify
> > them as possible as I can. so you can check them and comment easily.
> > Also, I was using nsnb=1 with ntb=1 only to remove the rotational and
> > transnational center of mass each step.
>
> nsnb is an outdated option dictating how frequently pairlist rebuilds are
> done. It has nothing to do with COM removal (that is nscm).
>
> > I know it is costly ! However, I am
> > planning to increase it upto 500 or remove it from the control file.
> > I am using force field of ff99 and the water model is TIP3PBOX.
>
> ff99 is 15+ years old, and has many well-known deficiencies that have been
> addressed in newer force fields. You choice of force field is MUCH more
> important than whether you remove COM motion every 1 or 500 steps, or
> whether you use SHAKE or not. I suggest you look at the discussion on
> force fields in the Amber14 manual to help inform which choice you should
> make.
>
> > The
> > conformational changes happened are favorable, expected and reasonable.
> > but I don't know if they are real time events or accelerated events. I
> > want to be able to claim or propose that this protein will behave
> similarly
> > in practical experiments.
>
> Many things can affect kinetic measurements, and no simulation technique
> except for strict NVE can preserve temporal properties (i.e., the use of a
> thermostat or any stochastic dynamics model ruins the time-continuity of
> your trajectory). Instead, I would use these simulations to characterize
> the free energy surface and use that surface to say something about
> expected transition rates between different states (you can compare *that*
> back to experiment).
>
> > What if I removed the shake from the production
> > md, do think that may slow down this conformational changes I got.
>
> No.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
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Received on Fri Feb 06 2015 - 05:00:02 PST
