[CP2K:6083] Topology error QMMM or MM
Teodoro Laino
teodor... at gmail.com
Wed Feb 11 20:56:58 UTC 2015
double check your PSF or PDB.. the error is self-esplicative : there must be two or more molecules that have the same name but have different atom sequence..
the fact your PSF or PDB may work with other codes means only that such codes are not performing tight checks.
Teo
> On 11 Feb 2015, at 18:51, cjor <chri... at gmail.com> wrote:
>
> Hello,
> I'm trying to run a QMMM simulation with CP2K based on a CHARMM FF MD simulation.
>
> I first tried to run MM to see it works, but I get the following error:
>
>
> "
> CP2K| version string: CP2K version 2.3
> CP2K| source code revision number: 12343
> CP2K| is freely available from http://www.cp2k.org/
> CP2K| Program compiled at Thu Feb 28 16:12:09 GMT 2013
> CP2K| Program compiled on popoca
> CP2K| Program compiled for Linux-x86-64-gfortran
> CP2K| Input file name mm.inp
>
> GLOBAL| Force Environment number 1
> GLOBAL| Basis set file name BASIS_SET
> GLOBAL| Geminal file name BASIS_GEMINAL
> GLOBAL| Potential file name POTENTIAL
> GLOBAL| MM Potential file name MM_POTENTIAL
> GLOBAL| Coordinate file name ionized.pdb
> GLOBAL| Method name CP2K
> GLOBAL| Project name phd2_md
> GLOBAL| Preferred FFT library FFTSG
> GLOBAL| Run type MD
> GLOBAL| All-to-all communication in single precision F
> GLOBAL| FFTs using library dependent lengths F
> GLOBAL| Global print level LOW
> GLOBAL| Total number of message passing processes 1
> GLOBAL| Number of threads for this process 1
> GLOBAL| This output is from process 0
>
> MEMORY| system memory details [Kb]
> MEMORY| rank 0 min max average
> MEMORY| MemTotal 132089732 132089732 132089732 132089732
> MEMORY| MemFree 2537384 2537384 2537384 2537384
> MEMORY| Buffers 407408 407408 407408 407408
> MEMORY| Cached 34948436 34948436 34948436 34948436
> MEMORY| Slab 732060 732060 732060 732060
> MEMORY| SReclaimable 581768 581768 581768 581768
> MEMORY| MemLikelyFree 38474996 38474996 38474996 38474996
>
> 49892 0
> Two molecules have been defined as identical molecules but atoms mismatch charges!!
> 49893 0
> Two molecules have been defined as identical molecules but atoms mismatch charges!!
> 49894 0
> Two molecules have been defined as identical molecules but atoms mismatch charges!!
> 49895 0
> Two molecules have been defined as identical molecules but atoms mismatch charges!!
> 49896 0
> Two molecules have been defined as identical molecules but atoms mismatch charges!!
> 49897 0
> Two molecules have been defined as identical molecules but atoms mismatch charges!!
> "
>
>
>
>
> I'm calling a PSF and PDF file that I know works. The error lies with the parsing of the
> ion section (SOD and CLA).
>
>
>
>
> My MM input is:
>
> &GLOBAL
> PRINT_LEVEL LOW
> PREFERRED_FFT_LIBRARY FFTSG
> PROJECT phd2_md
> RUN_TYPE MD
> &END GLOBAL
>
> &MOTION
> &MD
> ENSEMBLE NPT_I
> STEPS 6000
> TIMESTEP 0.48
> TEMPERATURE 298.0
> &THERMOSTAT
> TYPE NOSE
> REGION MASSIVE
> &NOSE
> TIMECON [wavenumber_t] 1000
> &END NOSE
> &END THERMOSTAT
> &PRINT
> &ENERGY
> FILENAME =phd2_md.ener
> &EACH
> MD 1
> &END EACH
> &END ENERGY
> &PROGRAM_RUN_INFO
> &EACH
> MD 1
> &END EACH
> &END PROGRAM_RUN_INFO
> &END PRINT
> &END MD
> &PRINT
> &TRAJECTORY
> FILENAME =phd2_md.xyz
> &EACH
> MD 1
> &END EACH
> &END TRAJECTORY
> &RESTART
> FILENAME =phd2_md.restart
> BACKUP_COPIES 1
> &EACH
> MD 10
> &END EACH
> &END RESTART
> &RESTART_HISTORY OFF
> &END RESTART_HISTORY
> &END PRINT
> &END MOTION
>
> &FORCE_EVAL
> METHOD FIST ! Using Molecular Mechanics
> &MM
> &FORCEFIELD
> parm_file_name par_all27_prot_lipid.inp
> parmtype CHM
> ei_scale14 1.0
> vdw_scale14 1.0
> &SPLINE
> emax_spline 1.0
> rcut_nb 12
> &END SPLINE
> &END FORCEFIELD
> &POISSON
> &EWALD
> ewald_type SPME
> alpha 0.44
> gmax 81
> &END EWALD
> &END POISSON
> &END MM
>
> &SUBSYS
> &CELL
> abc 80 80 80
> periodic xyz
> &END CELL
> &KIND H
> BASIS_SET DZVP-GTH-BLYP
> POTENTIAL GTH-BLYP-q1
> &END KIND
> &KIND O
> BASIS_SET DZVP-GTH-BLYP
> POTENTIAL GTH-BLYP-q6
> &END KIND
> &KIND N
> BASIS_SET DZVP-GTH-BLYP
> POTENTIAL GTH-BLYP-q5
> &END KIND
> &KIND C
> BASIS_SET DZVP-GTH-BLYP
> POTENTIAL GTH-BLYP-q4
> &END KIND
> &KIND Fe2
> BASIS_SET DZVP-MOLOPT-SR-GTH
> POTENTIAL DZVP-MOLOPT-SR-GTH
> &END KIND
>
> &TOPOLOGY
> CONNECTIVITY UPSF
> COORDINATE PDB
> COORD_FILE_NAME ionized.pdb
> CONN_FILE_NAME ionized.psf
> &END TOPOLOGY
> &END SUBSYS
> &END FORCE_EVAL
>
>
>
>
>
>
>
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