Dear Andy,
Thanks a lot for your answer, I'll give it a try!
All the best,
Ruth
On Saturday, January 27, 2018 00:20 CET, "Goetz, Andreas" <agoetz.sdsc.edu> wrote:
Dear Ruth,
You have to switch off Ewald summation and PME for QM-MM interactions by setting qm_ewald=0 in the &qmmm namelist. This truncates QM-MM electrostatic interactions and it is a good idea to increase qmcut to a large value. This is not ideal but the best you can currently do under PBC.
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 26, 2018, at 6:33 AM, Ruth Helena Tichauer <rhtichau.laas.fr> wrote:
>
> 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 - 22:00:02 PST
