Hi Abdullah,
It is not possible to use the QM/MM implementation for a full QM calculation under periodic boundary conditions. There is a separate implementation for semiempirical methods in AmberTools 19 that you can use instead (see section 10.5: SEBOMD in the Amber 19 manual). At present SEBOMD does not support PM6.
All the best,
Andy
—
Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de
> On Jan 3, 2020, at 8:43 AM, Abdullah Faheem <abdullah.bin.faheem.hotmail.com> wrote:
>
> 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 - 04:00:01 PST
