回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)
Christoph Riplinger
cri at thch.uni-bonn.de
Thu Nov 10 10:05:01 CET 2011
Dear Xi Zhao,
The ORCAINFO file is no tok. You should not give the Opt keyword there.
GMX is taking care of the optimization. If you provide the Opt keyword,
ORCA will do an optimization in each QM forces calculation, but
neglecting the QM-MM interactions, and this is not what you want.
So keep
! RKS B3LYP/G SV(P) TightSCF Opt
Hope that helps,
Christoph
On 11/07/2011 03:45 PM, xi zhao wrote:
> 4
> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>
> 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
> <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org>
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> > 1. orca and qm/mm (xi zhao)
> >
> >
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> ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 7 Nov 2011 20:54:04 +0800 (CST)
> > From: xi zhao <zhaoxiitc2002 at yahoo.com.cn
> <http://cn.mc151.mail.yahoo.com/mc/compose?to=zhaoxiitc2002@yahoo.com.cn>>
> > Subject: [gmx-users] orca and qm/mm
> > To: gmx-users at gromacs.org
> <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
> > Message-ID:
> > <1320670444.82465.YahooMailClassic at web15103.mail.cnb.yahoo.com
> <http://cn.mc151.mail.yahoo.com/mc/compose?to=1320670444.82465.YahooMailClassic@web15103.mail.cnb.yahoo.com>>
> > Content-Type: text/plain; charset="utf-8"
> >
> > All users:
> >
> >
> > According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code
> <http://wwwuser.gwdg.de/%7Eggroenh/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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