Re: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)
xi zhao
zhaoxiitc2002 at yahoo.com.cn
Tue Nov 8 13:48:36 CET 2011
When BASENAME.ORCAINFO has no coordinates of QMatoms, the mdrun showns "
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 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'
No atoms to convert in Cartesian2Internal"
When BASENAME.ORCAINFO has coordinates of QMatoms, such as "
!RKS BP RI SV(P) SV/J TightSCF Opt
* xyz -1 2
O 29.8300000 35.2700000 32.7900000
H 30.0700000 34.9700000 34.6300000
C 31.5600000 34.7800000 32.3000000
LA 31.7400000 34.8400000 30.8800000
.......
mdrun shows :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
how to write the BASENAME.ORCAINFO?
how to deal with LA ?
--- 11年11月8日，周二, 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8日,周二,下午4:19
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!
--- 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?
--- 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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> 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"
>
> 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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