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

limingru mruli at sina.com
Tue Sep 25 11:04:35 CEST 2018

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

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