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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>
>
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Received on Wed Jun 26 2019 - 00:00:03 PDT
