Dear AMBER users,
I am using AMBER 12 and I intend to run Semi-empirical QMMD using PM6 on a small box of an electrolyte mixture (60 molecules). I initially equilibrated my system using classical MD for 500 ps.
Input file for the Classical MD:
&cntrl
imin = 0, irest = 0, ntx = 1, ntpr = 500,
ntave = 1000, ntwr = 500, ntwx = 100,
ntwe = 50, ntf = 2, ntc = 2, ntb = 2,
cut = 8.0, nsnb = 10, nstlim = 500000,
dt = 0.001, tempi = 298.0, temp0 = 298.0,
ntt = 3, tautp = 1.0, ntp = 1, pres0 = 1.0,
taup = 1.0, ioutfm = 1, gamma_ln = 1, ig = -1,
&end
After the successful completion of the classical MD, I ran a QMMD on all molecules using PM6.
Input file for QMMD:
&cntrl
imin = 0, irest = 1, ntx = 5, ntpr = 10,
ntave = 20, ntwr = 10, ntwx = 10, ntwe = 5,
ntf = 2, ntc = 2, ntb = 2, ntp = 1,
cut = 8.0, nsnb = 10, nstlim = 1000,
dt = 0.001, tempi = 298.0, temp0 = 298.0,
ntt = 3, tautp = 1.0, taup = 1.0,
ioutfm = 1, gamma_ln = 1, ig = -1, ifqnt = 1,
/
&qmmm
qmmask = ':*',
qmcharge = 0,
qm_theory = 'PM6',
qmshake = 1,
qm_ewald = 1, qm_pme = 1,
/
However, I keep getting the error:
ERROR: QM region + cutoff larger than box dimension:
QM-MM Cutoff = 8.0000
Coord Lower Upper Size Radius of largest sphere inside unit cell
X -18.271 18.304 36.575 10.330
Y -18.300 18.282 36.582 10.330
Z -18.319 18.263 36.582 10.330
****************************************************
SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f>
QM region + cutoff larger than box
cannot continue, need larger box.
Is this because amber 12 does not allow QMMD on all the molecules in the system? If so, is there a reliable way around this?
Thank you for your help.
Regards,
Abdullah Bin Faheem
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Received on Fri Jan 03 2020 - 00:00:02 PST
