Re: [AMBER] QM/MM SMD with 'external' theory and PBCs

From: Goetz, Andreas <agoetz.sdsc.edu>
Date: Fri, 26 Jan 2018 23:20:53 +0000

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 - 15:30:02 PST
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