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
