To speedup GB simulation, you might want to use 'nrespa = 2' and 'rgbmax =
15' too.
Hai
On Sat, Dec 8, 2012 at 11:17 AM, Thomas Evangelidis <tevang3.gmail.com>wrote:
> Dear Amber community,
>
> I have prepared a system for implicit solvent simulation with an infinite
> cutoff (cut=999). Is there any way to control how often to construct the
> list with the pairs of atoms for which non-bonded interactions should be
> calculated? According to the manual the default behaviour (nbflag=1)
> updates the list whenever any atom has moved more than 1/2 skinnb since the
> last list update. Is there any way to deactivate that redundant check? For
> instance in NAMD there is a parameter named "staticAtomAssignment" which
> does exactly that thing (deactivates pairlist construction). The other way
> (nbflag=0) is not possible with implicit solvent (igb>0).
>
> Below is my parameter file. I would be grateful if anyone tells what
> changes I could do to speed up my simulation.
>
> thanks,
> Thomas
>
> &cntrl
>
> ! MOLECULAR DYNAMICS
> nstlim=1000, ! Number of MD-steps to be performed.
> dt=0.002,
> ntx=1, ! read coordinates and velocities from the restart file
> irest=0, ! this is not a simulation restart
> ntpr=100, ! print energy every 100 steps
> nrespa=1, ! evaluate forces every step
> ntwr=5000, ! write restart file (.restrt) every 5000 steps
> ntwx=5000, ! save coordinates every 5000
> ntb=0, ! no PBC with GB solvent
> igb=8, ! use the optimized GBn implicit solvent model (ibg=8)
> (better than simple GB [igb=1] or OBC[igb=2,5], although less tested)
> saltcon=0.15, ! salt concentration
>
> ! TEMPERATURE CONTROL
> tempi =100.0, ! initial temperature
> temp0=310.0, ! reference temperature at which the system is to be
> kept, if ntt > 0
> ntt=3, ! Use Langevin thermostat.
> gamma_ln=5, ! Damping coefficient for Langevin dynamics in ps - 1.
> tautp=2.0, ! Time constant, in ps, for heat bath coupling for the
> system, if ntt = 1
> ig=209858, ! The seed for the pseudo-random number generator
>
> ! PRESSURE CONTROL
> ! ntp=0, ! do not use pressure coupling
>
> ! BOND CONSTRAINTS
> ntc=2, ! bonds involving hydrogen are constrained with SHAKE
> tol=1.0e-8, ! Relative geometrical tolerance for coordinate resetting
> in shake
>
>
> ! ELECTROSTATICS & VDW
> ntf=2, ! ommit force evaluations for bond interactions involving
> H-atoms
> cut=999, ! Cut-off for vdW and electrostatic interactions.
>
> &end
>
> &ewald
>
> vdwmeth=1 ! Apply an analytical tail correction to the reported vdW
> energy and virial that is equal to the amount lost due to switching and
> cutoff
> ! of the LJ potential.
>
> &end
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Received on Mon Dec 10 2012 - 14:30:02 PST
