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

From: Ruth Helena Tichauer <rhtichau.laas.fr>
Date: Fri, 26 Jan 2018 15:33:05 +0100

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
  irest=1, ntx=5,
  ntb=2, pres0=1.0, ntp=1, taup=1.0,
  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',
  restraintmask = ':170,185,.CA,C,N',
  ifqnt=1, infe=1
  qmmask = ':168,169,179,196-197,3176,4085',
   output_file = 'nat2-0_smdg25-1_3176.txt'
   output_freq = 20

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,



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Received on Fri Jan 26 2018 - 07:00:03 PST
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