First, I would like to express my big gratefull for everyone for these
very usefull suggestions! Please find below some of my additional
questions.
Regarding berendsen thermostat - may the dynamics (e.g. transitions
observed for functionally-relevant domains, such as flexible loops of
enzymes) observed with this temperature coupling method be an
artifact, expecially in the cases when I do simulations at high
temperatures (330, 350, 400K) or alternatively using accelerated MD?
Regarding, langevin's dynamics- may I run production run for the
perdiod of 100 ns without restarting system using random seed ? Would
it be neccesary step-by-step decrease gamma_ln during the
equilibration in order to equilibrate flexible system (which consist
of several long loops, for instance)?
Yours with thanks,
Professor James Starlight
ср, 26 июн. 2019 г. в 21:09, David Cerutti <dscerutti.gmail.com>:
>
> 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.
> > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> >
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Received on Thu Jun 27 2019 - 01:30:03 PDT
