On Sun, Aug 24, 2014 at 1:42 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 *
>
Why are you switching GB models and cutoffs? This is a bad idea generally
-- you should almost always use the same Hamiltonian for every step of your
simulation. And ntt=1 is also a bad choice for thermostat in implicit
solvent. ntt=3 is better.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Aug 24 2014 - 07:30:02 PDT
