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. 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. 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. What if I removed the shake from the production
md, do think that may slow down this conformational changes I got.
Regards
Hadeer ELHabashy
On Thu, Feb 5, 2015 at 2:55 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> > On Feb 5, 2015, at 6:49 AM, Hadeer ELHabashy <hadeer.elhabashi.gmail.com>
> wrote:
> >
> > Dear Sir
> >
> > wish you are fine !
> >
> > I am running a MDS protocol on a protein in a water box expecting some
> > conformational changes. I've got some favorable conformation changes
> > started with starting the simulation and continues until 100 ns of
> > simulation and beyond . with 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
> >
> > The question now : depending on the mentioned protocol
> > can you see any failure in the previous protocol ?
>
> Not at quick glance, but these input files are too long to do a careful
> study of them. You set many variables that you don’t use to their default
> value (like ntwe=0 and ntwv=0, to name two), along with other variables
> that I’ve never used before and an unfamiliar with (e.g., iesp=0, t=0.0,
> and I can never remember the difference between jfastw=0 and jfastw=4),
> which makes it difficult to grok your input files.
>
> If these input files work for you, that’s great. But if you plan on
> requesting an audit of your input files -- either from here or someone else
> -- you should simplify them as much as possible so that every variable that
> you specify is significant to your simulation. That makes it easier for the
> people from whom you ask for help and increases the likelihood that they
> will find a mistake if you made one.
>
> > can I consider these changes in protein conformation as real time events
> ?
>
> Maybe. It could also be a force field artifact or some other artifact of
> your system setup. You would know better than us if that was likely or if
> what you are seeing seems reasonable.
>
> > what are the parameters of the MD control file that can decelerate or
> > accelerate a real time event ?
>
> You can *accelerate* stuff using enhanced sampling techniques, like
> accelerated MD, umbrella sampling, steered MD, or replica exchange (to name
> a few approaches). These are advanced topics, though, so you would need to
> invest time into learning the underlying theory behind the methods as well
> as learning how to run and analyze the simulations in Amber. I’m not sure
> why anybody would ever want to decelerate sampling, and there’s no way to
> really do that. You could, of course, drop the temperature very low so
> everything moves slower, increase the mass of every atom to get a similar
> effect, or decrease the time step so each *MD* step doesn’t move as far in
> time (limiting how *far* it can move). But the first two changes the
> system you’re studying so that the final answers will not necessarily be
> the same, and the last doesn’t actually make the sampling go any slower per
> ns of simulation; it just makes each ns of simulation take more steps to
> complete.
>
> > does the applied shake ,providing that all the bond interaction involving
> > hydrogen bonding are omitted, affect the real time event ?
>
> It’s unclear what “effects” you are curious about. It certainly affects
> any events dependent on H- bond vibrations, but no examples come to my
> mind. For most events, I don’t think SHAKE has a significant effect
> (except in cases where it is required, like with the TIPnP rigid water
> models).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
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Received on Thu Feb 05 2015 - 11:00:03 PST
