[CP2K:6156] Topology error QMMM or MM

Christian Jorgensen chri... at gmail.com
Thu Feb 12 21:52:00 UTC 2015
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My apologies. I've reported it now.
 On 12 Feb 2015 21:47, "Teodoro Laino" <teodor... at gmail.com> wrote:

> Which tone? If you believe that you have a problem with psfgen you should
> report this to the psfgen mailing list.
>
> On 12 Feb 2015, at 15:07, Christian Jorgensen <chri... at gmail.com> wrote:
>
> Sorry I do not understand why the tone on
> this board is like this. I'm simply asking for help.
>
>
>
>
>
> On Thu, Feb 12, 2015 at 7:16 AM, Teodoro Laino <teodor... at gmail.com>
> wrote:
>
>> report this to the proper mailing list.
>>
>> On 11 Feb 2015, at 23:04, Christian Jorgensen <chri... at gmail.com>
>> wrote:
>>
>> ATOM  49880  SOD SOD I  37      21.151   0.526 -30.628  1.00  0.00
>>  ION NA
>> ATOM  49881  SOD SOD I  38      24.667 -35.051  19.114  1.00  0.00
>>  ION NA
>> ATOM  49882  SOD SOD I  39     -12.620   2.426  26.969  1.00  0.00
>>  ION NA
>> ATOM  49883  SOD SOD I  40     -10.705 -33.380 -11.158  1.00  0.00
>>  ION NA
>> ATOM  49884  SOD SOD I  41     -19.491  29.350 -34.679  1.00  0.00
>>  ION NA
>> ATOM  49885  SOD SOD I  42      40.802 -30.866  10.911  1.00  0.00
>>  ION NA
>> ATOM  49886  SOD SOD I  43     -21.411 -20.389  17.270  1.00  0.00
>>  ION NA
>> ATOM  49887  SOD SOD I  44      13.100  24.287  18.857  1.00  0.00
>>  ION NA
>> ATOM  49888  SOD SOD I  45      33.628  30.716  18.333  1.00  0.00
>>  ION NA
>> ATOM  49889  SOD SOD I  46      14.256 -31.556  -9.097  1.00  0.00
>>  ION NA
>> ATOM  49890  SOD SOD I  47      -1.600  38.825  28.079  1.00  0.00
>>  ION NA
>> ATOM  49891  SOD SOD I  48      26.911  -9.319  19.217  1.00  0.00
>>  ION NA
>> ATOM  49892  CLA CLA I  49     -21.849 -29.233  -4.389  1.00  0.00
>>  ION CL
>> ATOM  49893  CLA CLA I  50     -27.778  19.207  -8.907  1.00  0.00
>>  ION CL
>> ATOM  49894  CLA CLA I  51      -1.036 -18.525 -33.557  1.00  0.00
>>  ION CL
>> ATOM  49895  CLA CLA I  52     -37.955  23.751  -9.529  1.00  0.00
>>  ION CL
>> ATOM  49896  CLA CLA I  53     -15.636 -34.005  12.873  1.00  0.00
>>  ION CL
>> ATOM  49897  CLA CLA I  54      40.122  21.296 -26.349  1.00  0.00
>>  ION CL
>> ATOM  49898  CLA CLA I  55      32.593  -9.101  17.836  1.00  0.00
>>  ION CL
>> ATOM  49899  CLA CLA I  56       8.168 -24.215   8.246  1.00  0.00
>>  ION CL
>> ATOM  49900  CLA CLA I  57      -4.530 -32.691  -6.031  1.00  0.00
>>  ION CL
>> ATOM  49901  CLA CLA I  58     -14.998  37.422   2.603  1.00  0.00
>>  ION CL
>> ATOM  49902  CLA CLA I  59     -22.559 -24.866 -37.160  1.00  0.00
>>  ION CL
>> ATOM  49903  CLA CLA I  60      22.442 -17.653 -37.184  1.00  0.00
>>  ION CL
>> ATOM  49904  CLA CLA I  61     -31.657   0.756 -22.411  1.00  0.00
>>  ION CL
>> ATOM  49905  CLA CLA I  62     -25.707   4.569  26.200  1.00  0.00
>>  ION CL
>> ATOM  49906  CLA CLA I  63       9.816  21.844 -29.523  1.00  0.00
>>  ION CL
>> ATOM  49907  CLA CLA I  64      20.348  15.655  31.373  1.00  0.00
>>  ION CL
>> ATOM  49908  CLA CLA I  65     -33.471  28.927  25.816  1.00  0.00
>>  ION CL
>> ATOM  49909  CLA CLA I  66     -23.076 -36.320 -14.581  1.00  0.00
>>  ION CL
>> ATOM  49910  CLA CLA I  67      11.228  23.055  26.442  1.00  0.00
>>  ION CL
>> ATOM  49911  CLA CLA I  68     -31.967 -25.220  12.122  1.00  0.00
>>  ION CL
>> ATOM  49912  CLA CLA I  69       7.122 -32.163 -23.902  1.00  0.00
>>  ION CL
>> ATOM  49913  CLA CLA I  70     -30.542 -17.921  15.502  1.00  0.00
>>  ION CL
>> ATOM  49914  CLA CLA I  71     -35.163 -32.044  11.857  1.00  0.00
>>  ION CL
>> ATOM  49915  CLA CLA I  72      -1.340 -18.251 -21.790  1.00  0.00
>>  ION CL
>>
>>
>> In relation to the error
>>
>>
>>        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!!
>> "
>>
>>
>> How can this be? I've generated this with the standard PSFGEN / Ionize
>> plugin written
>> for VMD.
>>
>>
>>
>>
>>
>>
>>
>>
>> On Wed, Feb 11, 2015 at 9:14 PM, Christian Jorgensen <chri... at gmail.com
>> > wrote:
>>
>>> Hello Dr Laino
>>>
>>> This is a problem with the ions. The atom indices it is warning about
>>> are all chlorine added to achieve electrical neutrality ( in VMD with
>>> Psfgen for NAMD)
>>>
>>> I do not understand because I've used the standard procedure from Psfgen
>>> On 11 Feb 2015 20:57, "Teodoro Laino" <teodor... at gmail.com> wrote:
>>>
>>>> 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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>>>
>>
>>
>> --
>> _______
>>
>> Christian Jørgensen
>>
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>
>
>
> --
> _______
>
> Christian Jørgensen
>
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