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

xi zhao zhaoxiitc2002 at yahoo.com.cn
Tue Nov 8 08:07:38 CET 2011


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"
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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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