On Tue, Jan 26, 2016 at 4:01 PM, Covington, Cody Lance <
cody.l.covington.vanderbilt.edu> wrote:
> Hello
>
> I am trying to simulate a system of dimer molecules in the gas phase. When
> I turn off the periodic boundaries with ntb=0 it will work but every so
> often (100-500 ps) it dissociates and I get the error:
>
>
> NSTEP = 82000 TIME(PS) = 164.000 TEMP(K) = 474.01 PRESS =
> 0.0
> Etot = 35.8464 EKtot = 107.3817 EPtot =
> -71.5353
> BOND = 20.8605 ANGLE = 75.8173 DIHED =
> 41.7257
> 1-4 NB = 20.8793 1-4 EEL = -82.8782 VDWAALS =
> 2.7036
> EELEC = -150.6434 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ------------------------------------------------------------------------------
>
> Frac coord min, max: 0.236659570259939 1.00005584928049
> The system has extended beyond
> the extent of the virtual box.
> Restarting sander will recalculate
> a new virtual box with 30 Angstroms
> extra on each side, if there is a
> restart file for this configuration.
> SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
> Atom out of bounds. If a restart has been written,
> restarting should resolve the error
>
> Is there any way to define a rigid boundary?
>
Not in a general way. You can set igb=6 to get gas-phase simulations to
run in the GB code, which doesn't have any requirement that a virtual box
exist (so you will therefore never run into this issue).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jan 26 2016 - 14:30:03 PST
