回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)
Micha Ben Achim Kunze
ucbtmbk at live.ucl.ac.uk
Tue Nov 8 09:19:01 CET 2011
I am not sure I understand exactly what you mean but this is all covered
in Gerrit's QM/MM tutorials, I'd recommend you go through those. In the
ORCA files there is no need to do anything with LAs, GMX will hand a
file with the QMsubsystem to ORCA which includes the LA as hydrogens in
your case I guess.
Cheers,
Micha
On 08/11/11 07:07, xi zhao wrote:
> Thank you for your suggest, my gromacs reinstalled: ./configure --
> --without-qmmm-gaussian --without-qmmm-orca ....
> when mpirun -np 1 mdrun_p -v -s pyp_qm.tpr,
>
> Back Off! I just backed up md.log to ./#md.log.1#
> Getting Loaded...
> Reading file pyp_qm.tpr, VERSION 4.5.3 (double precision)
> Loaded with Money
> QM/MM calculation requested.
> there we go!
> Layer 0
> nr of QM atoms 22
> QMlevel: RHF/3-21G
> /home/user/orca_x86_64_exe_r2131/home/user/orca_x86_64_exe_r2131...
> orca initialised...
> Back Off! I just backed up traj.trr to ./#traj.trr.1#
> Back Off! I just backed up traj.xtc to ./#traj.xtc.1#
> Back Off! I just backed up ener.edr to ./#ener.edr.1#
> starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water'
> 500 steps, 0.5 ps.
> Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp >> pyp_qm.out'
> Unless this is specifically allowed this means that the basis set
> is not
> available for this element - Aborting the run
> -------------------------------------------------------
> Program mdrun_p, VERSION 4.5.3
> Source code file: qm_orca.c, line: 409
> Fatal error:
> Call to '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp >>
> pyp_qm.out' failed
> ......
> but a question raised: how to deal with LA in the QMatoms in orca
> inputfile? using DA ( dummy atom in the ORCA) repaces LA in the
> QMatoms in the gromacs ?
> please give me a suggestion!
> Thank you!
> 4
> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>
> --- *11年11月7日，周一, Micha Ben Achim Kunze
> /<ucbtmbk at live.ucl.ac.uk>/* 写道：
>
>
> 发件人: Micha Ben Achim Kunze <ucbtmbk at live.ucl.ac.uk>
> 主题: Re: 回复： [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10:50
>
> 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>
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=ggroenh@gwdg.de>/*
>> 写道：
>>
>>
>> 发件人: Gerrit Groenhof <ggroenh at gwdg.de>
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=ggroenh@gwdg.de>
>> 主题: [gmx-users] Re 1. orca and qm/mm (xi zhao)
>> 收件人: gmx-users at gromacs.org
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@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>
>> wrote:
>>
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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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