[gmx-users] GROMACS/CPMD QMMM do not occur the process of the hydrogen abstraction reaction

[limingru]

Dear all, 	I'm doing the QMMM simulation about OH radicals interacting with DNA's base (Guanine) by using GMX-CPMD package. Based on the paper "Multiscale QM/MM Molecular Dynamics Study on the First Steps of Guanine Damage by Free Hydroxyl Radicals in Solution (web site: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3356683/)", there is no the process of the hydrogen abstraction reaction in my simulation. Please see the related content of the CPMD_inp.tmpl. I tried to modify my parameter file for a long time, but this reaction is not alway occured. So I wish get some relevant researchers' advices. Thanks in advance.

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School of Nuclear Sci and Tec,
Beijing Normal University

Room.110,Teaching-Research Complex,
NO.10 WenHuiYuan St,Haiding District,
Beijing 100089,China  

E-mail: mruli at sina.com 
        mruli at mail.bnu.edu.cn
Tel: +86-138-828-55737



----- Original Message -----
From: "limingru" <mruli at sina.com>
To: "gromacs.org_gmx-users" <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: GROMACS/CPMD wavefunction optimize
Date: 2018-06-07 10:58

Hi everyone,	I'm trying to study on the damage of base by free hydroxyl radicals using GROMACS-CPMD program. However, error occurred in optimization of wave function. Would everyone tell me wheher the interface GMX and the OPTIMIZE option cannot be used at the same time? if permitted, How did I do?  Please see the relatedcontent of the CPMD_inp.tmpl and em.mdp. Thanks in advance.
#CPMD_inp.tmpl&CPMD
   INTERFACE GMX PCGFIRST
   MOLECULE CENTER OFF
   PCG MINIMIZE
   OPTIMIZE WAVEFUNCTION
   LSD
&END

&DFT
  FUNCTIONAL BLYP
  GRADIENT CORRECTION BECKE88 LYP
  LDA CORRELATION LYP
  GC-CUTOFF
  1.D-6
&END

&SYSTEM
   POISSON SOLVER TUCKERMAN
   SYMMETRY
   0
   ANGSTROM
   CELL 
   29.555 0.6398 0.92862 0.0 0.0 0.0
   MULTIPLICITY
   2
   CUTOFF
   40.0
   CHARGE
   -0.40999
&END

&ATOMS
*H_VDB_PBE.psp FORMATTED
  LMAX=S
*O_VDB_PBE.psp FORMATTED
  LMAX=P
*C_VDB_PBE.psp FORMATTED
  LMAX=P
*N_VDB_PBE.psp FORMATTED
  LMAX=P
&END
#em.mdpconstraints         =  all-bonds
integrator          =  steep
constraint_algorithm= shake
QMMM                =  yes
QMmethod            =  CPMD
QMMMscheme          =  normal
QMMM-grps           =  QM 
QMbasis             =  STO-3G
QMcharge          = -0.40999
QMmult             = 2
planewavecutoff     =  45
qmmmcoul_cutoff     =  45
MMlayer_radii       =  10 10
MMlayer_updfqs      =  1  1
qmbox_cpmd          =  29.555 18.91 27.445
--------------------------------


School of Nuclear Sci and Tec,
Beijing Normal University

Room.110,Teaching-Research Complex,
NO.10 WenHuiYuan St,Haiding District,
Beijing 100089,China  

E-mail: mruli at sina.com 
        mruli at mail.bnu.edu.cn
Tel: +86-138-828-55737