I don't know about high-T simulations with Berendsen but I imagine that any
problems would be magnified. You don not need to iteratively decrease
gamma_ln during an equilibration--any state that you get form Langevin
dynamics will be legitimate, it's just that the succession between states
will not follow a representative course of a system acting only according
to its own internal forces. You can run for 100ns at a time, but you
cannot change most of the thermostating conditions over that time, nor
should it be necessary. Equilibrate, then produce.
Dave
On Thu, Jun 27, 2019 at 4:18 AM James Starlight <jmsstarlight.gmail.com>
wrote:
> 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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Received on Thu Jun 27 2019 - 09:00:02 PDT
