Yes, to avoid problems with repeating random seeds simply set ig = -1.
However, to reproduce the results exactly you would need to extract the
random seeds that were actually used from the mdout files (it will say the
number down below the reprint of the input file). It probably isn't a big
deal to get an exact retrace of the dynamics in your case.
Dave
On Wed, Jun 26, 2019 at 1:55 PM Matias Machado <mmachado.pasteur.edu.uy>
wrote:
> Dear James,
>
> Answering your question, yes (ig=-1,) is a convenient the way to set a new
> random seed each restart... in addition you shouldn't want to run extremely
> long simulations using the same seed cause there doesn't exist true random
> chains, hence they periodically repeats giving enough time... this means
> restarting the MD from time to time is a good thing to add noise into the
> system...
>
> This is just some literature to add on David's comments...
>
> Anomalous Effects of Velocity Rescaling Algorithms: The Flying Ice Cube
> Effect Revisited, JCTC, 2018
> [https://pubs.acs.org/doi/abs/10.1021/acs.jctc.8b00446]
>
> In short, authors suggest never using Berendsen thermostat for
> production...
>
> Best,
>
> Matias
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "James Starlight" <jmsstarlight.gmail.com>
> Para: "AMBER Mailing List" <amber.ambermd.org>, dscerutti.gmail.com
> Enviados: Miércoles, 26 de Junio 2019 3:39:33
> Asunto: Re: [AMBER] Modeling of flexible enzyme: on the selection of the
> thermostat
>
> Thanks so much, David for the suggestions regarding simulations with
> Langevin's dynamics!
>
> Could you precise more about "not restarting the simulation with the
> same random seed"
>
> Does it means just that on each step (e.g. when I equilibrate sysytem
> decreasing restraints applied on protein or alternatively go from
> equilibration to production run) I should to include the following
> option (ig=-1,) in my input file, shouldn't it?
>
>
> Here the example of equilibration routine
> ; equilibration with LAngevins dynamics with 25 kcal/mol restraints
> on protein at constant T= 310K & P= 1Atm and coupling constant = 0.2
> ; gamma_ln=5.0, for equilibration;
> &cntrl
> imin=0, ntx=5, ntpr=500, ntwr=500, ntwx=500, ntwe=500,
> nscm=5000,
> ntf=2, ntc=2,
> ntb=2, ntp=1, tautp=0.2, taup=0.2,
> nstlim=25000, t=0.0, dt=0.002,
> cut=9.0,
> ntt=3, gamma_ln=5.0, ig=-1,
> iwrap=1,
> irest=1,
> ntr=1,
> temp0=310.0
> restraint_wt=25.0, restraintmask='(:1-200)&(.CA,C,O,N)'
> /
> &end
>
> ; and here how I do production run after several equilibrations step
> ; note than I increase here gamma_ln
> ; MD without restraints during 20ns at constant T= 310K & P= 1Atm
> &cntrl
> imin=0, ntx=5, ntpr=5000, ntwr=5000, ntwx=5000, ntwe=5000,
> nscm=5000,
> ntf=2, ntc=2,
> ntb=2, ntp=1, tautp=1.0, taup=0.5,
> nstlim=500000, t=0.0, dt=0.002,
> cut=9.0,
> ntt=3, gamma_ln=1.0, ig=-1,
> iwrap=1,
> irest=1,
> temp0=310.0
> &end
>
> >
> > Prof. Starlight Jr.,
> >
> > This may or may not help you:
> https://pubs.acs.org/doi/abs/10.1021/acs.biochem.6b00130
> >
> > We modeled the flexibility of xylanase B2, we found that NVE ensemble
> without a thermostat is appropriate. It appears that applying thermostat
> (or barostat) may influence the dynamics of proteins.
> >
> > Pratul
> >
> > Pratul K. Agarwal, Ph.D.
> > (Editorial Board Member: PLoS ONE, Microbial Cell Factories)
> > Web: http://www.agarwal-lab.org/
> >
> > On 6/25/2019 2:20 PM, James Starlight wrote:
> >
> > Dear Amber Users!
> >
> > At present moment, I am dealing with the modeling of the enzymes from
> > xylanase subfamily, which have several flexible loops of crusial
> > functional importance in shielding of the active site and thus in
> > being significative for tayloring of the enzyme to its substrate.
> >
> > Could you tell me which thermostat that had been emplemented in Amber
> > should be better option to reproduse dynamics of such inherently
> > dynamical systems (with flexible loops) assuming that I model it with
> > complex with substrate (sugar, parametrized by GLYCAM) as well as in
> > the apo-state?
> >
> > Notably, actually I have tried to use Berendsen method, which probably
> > was not good solution for the modeling in nanosecond range.
> >
> > # equilibrate
> > ntt=1, tempi=0.5, temp0=310.0,
> > #run production
> > ntt=1, tempi=0.1, temp0=310.0,
> >
> > May the switching to Langeving dynamics in the following manner be
> > better for the modeling of such system?
> >
> > #run equilibration
> > ntt=3, temp0=310, gamma_ln=5
> > #run production
> > ntt=3, temp0=310, gamma_ln=1
> >
> > Yours with thanks,
> >
> > Prof. James Starlight Jr.
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
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Received on Wed Jun 26 2019 - 12:30:02 PDT
