回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)
Micha Ben Achim Kunze
ucbtmbk at live.ucl.ac.uk
Mon Nov 7 15:50:57 CET 2011
From the output it looks like you forgot the --without-qmmm-gaussian
flag while compiling.
Micha
On 07/11/11 14:42, xi zhao wrote:
> When remove these lines, the errros still :Fatal error:
> Invalid QMMM input: 1 groups 0 basissets and 0 methods;
> when put something there, (
> QMmethod =rhf;QMbasis =sto-3g),
>
> grompp_a -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o pyp_qm.tpr
> -maxwarn 10
> mpirun -np 8 mdrun_a -v -s pyp_qm.tpr
> ......
> Back Off! I just backed up md.log to ./#md.log.7#
> Getting Loaded...
> Reading file pyp_qm.tpr, VERSION 4.5.3 (double precision)
> Loaded with Money
> QM/MM calculation requested.
> QM/MM calculation requested.
> QM/MM calculation requested.
> QM/MM calculation requested.
> QM/MM calculation requested.
> QM/MM calculation requested.
> there we go!
> QM/MM calculation requested.
> QM/MM calculation requested.
> there we go!
> there we go!
> there we go!
> there we go!
> there we go!
> there we go!
> there we go!
> Layer 0
> nr of QM atoms 22
> QMlevel: RHF/STO-3G
> number of CPUs for gaussian = 1
> memory for gaussian = 50000000
> accuracy in l510 = 8
> NOT using cp-mcscf in l1003
> Level of SA at start = 0
> -----------------------------------------------------------------------------
> One of the processes started by mpirun has exited with a nonzero exit
> code. This typically indicates that the process finished in error.
> If your process did not finish in error, be sure to include a "return
> 0" or "exit(0)" in your C code before exiting the application.
> PID 11786 failed on node n0 (127.0.0.1) due to signal 11.
> how to deal with?
> 4
> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
> --- *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)
> >
> >
> >
> ----------------------------------------------------------------------
> >
> > 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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