Dear Dave,
thanks so much again for your useful suggestions!
I am only wondering about selection of the tautp with ntt=3
(langevin's dynamics), while using gamma_ln=1.0 for the production
runs.
Normally, increasing the value of tautp should result in greater
coupling with thermal bath. On the other
hand to have less effect from the thermostat on the dynamics of the
system, the smaller value should be used, doesn't it? Othervise,
should tautp be ignored with ntt=3 ?
James
чт, 27 июн. 2019 г. в 17:34, David Cerutti <dscerutti.gmail.com>:
>
> 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 Wed Jul 03 2019 - 06:30:03 PDT
