[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.#CPMD_inp.tmpl&DFT    FUNCTIONAL BLYP    GRADIENT CORRECTION BECKE88 LYP    LDA CORRELATION LYP    GC-CUTOFF    5.D-5&END&SYSTEM   SYMMETRY   0   CELL    15.0 1.0 1.0 0.0 0.0 0.0   CUTOFF   30.0   MULTIPLICITY   2&END&ATOMS*H_VDB_BLYP.psp FORMATTED  LMAX=S*O_VDB_BLYP.psp FORMATTED  LMAX=P*C_VDB_BLYP.psp FORMATTED  LMAX=P*N_VDB_BLYP.psp FORMATTED  LMAX=P&END
--------------------------------


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