回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)

[xi zhao]

in addition, how to write ORCAINFO?  Is my file right?

! RKS B3LYP/G SV(P) TightSCF Opt  or  RKS B3LYP/G SV(P) TightSCF Opt  


--- 11年11月7日，周一, Gerrit Groenhof <ggroenh at gwdg.de> 写道：


发件人: Gerrit Groenhof <ggroenh at gwdg.de>
主题: [gmx-users] Re 1. orca and qm/mm (xi zhao)
收件人: gmx-users at gromacs.org
日期: 2011年11月7日,周一,下午9:23


Try to remove these lines, or put something there. The input is ignored, but since strings are used as input (for use in multui-layer oniom), leaving blank causes an error.

Gerrit
On 7 Nov 2011, at 14:21, gmx-users-request at gromacs.org wrote:

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>   1. orca and qm/mm (xi zhao)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Mon, 7 Nov 2011 20:54:04 +0800 (CST)
> From: xi zhao <zhaoxiitc2002 at yahoo.com.cn>
> Subject: [gmx-users] orca and qm/mm
> To: gmx-users at gromacs.org
> Message-ID:
>     <1320670444.82465.YahooMailClassic at web15103.mail.cnb.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
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> All users:
> 
>  
> According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code, I want to build qm/mm calculation by using gromacs 4.5.3 + orca 2.8.0. I set up the BASENAME, ORCA_PATH and  BASENAME.ORCAINFO as told in the instruction. 
> BASENAME=pyp_qm
> here is the BASENAME.ORCAINFO file:
> ! RKS B3LYP/G SV(P) TightSCF Opt
>  
> here is the md file:
> integrator               = md
> tinit                    = 0
> dt                       = 0.001
> nsteps                   = 500
> nstcomm                  = 1
> comm_grps                = system
>  
> emtol                    = 100.0
> emstep                   = 0.001
> nstcgsteep               = 50
>  
> nstxout                  = 1
> nstvout                  = 1
> nstfout                  = 1
> nstlog                   = 1
> nstenergy                = 1
> nstxtcout                = 1
> xtc_grps                 = system
> energygrps               = QMatoms rest_Protein SOL
>  
> nstlist                  = 10
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.0
>  
> coulombtype              = cut-off
> rcoulomb                 = 1.4
> epsilon_r                = 1
> vdwtype                  = Cut-off
> rvdw                     = 1.4
>  
> tcoupl                   = berendsen
> tc-grps                  = rest_Protein SOL QMatoms
> tau_t                    = 0.1 0.1 0 ; QM atoms are uncoupled
> ref_t                    = 300 300 300
> Pcoupl                   = Berendsen
> pcoupltype               = isotropic
> tau_p                    = 1.0
> compressibility          = 4.5e-5
> ref_p                    = 1.0
>  
> free_energy              = no
> init_lambda              = 0
> delta_lambda             = 0
> QMMM                     = yes
> QMMM-grps                = QMatoms
> QMmethod                 =
> QMbasis                  =
> QMMMscheme               = normal
> QMcharge                 = -1
> CASelectrons             =
> CASorbitals              =
> SH                       =
>  
> gen_vel                  = no
> gen_temp                 = 300
> gen_seed                 = 173529
>  
> constraints              = all-bonds
> constraint_algorithm     = LINCS
> unconstrained_start      = yes
> shake_tol                = 0.0001
> lincs_order              = 4
> lincs_warnangle          = 30
> morse                    = no
>   According to the instruction “In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given. (This also means that QMmethod and QMbasis from the mdp-file are ignored).”, the QMmethod and QMbasis are blank, 
>    But When grompp
> grompp_c -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o pyp_qm.tpr
> ……….
> Fatal error:
> Invalid QMMM input: 1 groups 0 basissets and 0 methods.
>  
> How to deal with it? Please help me!
> 
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