What is the goal of the simulation? What type of molecule are you
simulating? Implicit solvents have different strengths and weaknesses and
which one you choose depends on your goals (the same goes for many other
options in your simulation, it's why amber has more than 1 choice for many
settings).
On Aug 24, 2014 1:43 AM, "Bajarang Kumbhar" <kumbharbajarang.gmail.com>
wrote:
> *Dear ALL AMBER USER *
> I want to do simulation of protein using IMPLICIT method and i am new
> regarding this one.
> I have used this protocol for implicit MD*. *
>
> Minimization -> Heating -> Equilibration -> production MD.
>
> *(please help me regarding to setup implicit simulation)*
>
> *I have used this file.........*
>
> *Minimization of protein*
> *&cntrl *
> *imin=1, maxcyc=2000, ncyc=1000, *
> *cut=999.0, **igb=5,ntb=0, *
> *ntc=2,ntf=2, **ntpr=100, *
> *ntr=1, restraintmask=':1-438, *
> *restraint_wt=50.0 *
>
>
>
>
>
>
>
>
>
>
>
> *Heating of system&cntrl imin=0,irest=0,ntx=1, nstlim=100000, dt=0.001,
> ntc=2,ntf=2, cut=999.0, igb=5,ntb=0, ntpr=1000, ntwx=0, ntt=3,
> gamma_ln=2.0, tempi=0.0, temp0=300.0, ntr=1, restraintmask=':1-438',
> restraint_wt=5.0, nmropt=1 / &wt TYPE='TEMP0', istep1=0, istep2=100000,
> value1=0.1, value2=300.0, / &wt TYPE='END' / *
>
> *equilibration file: *
>
> *imin=0,** igb=2, cut=20.0,** ntr=1, intdiel=1.0 , extdiel=78.5, ntb=0,
> nstlim=20000, dt=0.002, ntc=2, ntf=2,*
> * tempi=10.0, temp0=300.0,** ntt=1,** tautp=2.0,** ntp=0,** ntpr=100,
> ntwx=0 *
>
> Thanks
>
> --
>
> *Dr. Bajarang V. Kumbhar* M.Sc.
> Ph.D
> Post-Doctoral Fellow
> Lab-204, Biophysics and Computational Biology,
> Department of Biosciences and Bioengineering,
> Indian Institute of Technology Bombay, Powai Mumbai-400076
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>
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Received on Sun Aug 24 2014 - 08:30:02 PDT
