[AMBER] Implicit solvent simulation study

From: Bajarang Kumbhar <kumbharbajarang.gmail.com>
Date: Sun, 24 Aug 2014 11:12:54 +0530

     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 *


*Dr. Bajarang V. Kumbhar*                                          M.Sc.
Post-Doctoral Fellow
Lab-204, Biophysics and Computational Biology,
Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai Mumbai-400076
AMBER mailing list
Received on Sat Aug 23 2014 - 23:00:02 PDT
Custom Search