[AMBER] how to speed up implicit solvent simulation with infinite cutoff

From: Thomas Evangelidis <tevang3.gmail.com>
Date: Sat, 8 Dec 2012 18:17:40 +0200

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 Sat Dec 08 2012 - 08:30:02 PST
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