Dear Amber users,
I’m trying to run a QM/MM SMD simulation of a protein complex in explicit solvent (with Periodic Boundary Conditions), using the following input file:
SMD LCOD rxn coord using Gaussian
&cntrl
imin=0,
irest=1, ntx=5,
ntb=2, pres0=1.0, ntp=1, taup=1.0,
cut=12.0,
tempi=300.0, temp0=300.0,
ntt=3, gamma_ln=2.0, ig=-1,
nstlim=100000, dt=0.0005,
ntpr=100, ntwx=100, ntwr=1000, ioutfm=1,
ntc=2, ntf=2,
noshakemask = '.2646-2689,2828-2851,2941-2946,11881-11883,14608-14610',
ntr=1,
restraintmask = ':170,185,.CA,C,N',
restraint_wt=5.0,
ifqnt=1, infe=1
/
&qmmm
qmmask = ':168,169,179,196-197,3176,4085',
qmcharge=0,
qm_theory='EXTERN',
qmshake=0,
qmcut=8.0,
/
&gau
method='B3LYP',
basis='6-31G**',
num_threads=8,
mem='500MW',
/
&smd
output_file = 'nat2-0_smdg25-1_3176.txt'
output_freq = 20
cv_file='cv_nat2-0-1_3176.in'
/
As PME is not supported for external QM softwares, I’m getting the following error.
SANDER BOMB in subroutine read_qmmm_nm_and_alloc
qm_theory=EXTERN but qm_ewald /= 0.
The external interface does not currently support EWALD or PME
Thus I would like to know how I should change my input file in order for it to work, keeping the PBCs:
_ Should I add qm_pme=0 although it is recommended for testing purposes only
_Should I add qm_ewald=0 although it is the default for non-periodic simulations (so I wonder if it is suitable when using PBCs)
_Should I change the qm cutoff qmcut (if yes, which value would you recommend for it?
Thank you for any insight into this matter,
Sincerely,
Ruth
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Received on Fri Jan 26 2018 - 07:00:03 PST
