[CP2K:6087] Topology error QMMM or MM

Teodoro Laino teodor... at gmail.com
Thu Feb 12 07:16:33 UTC 2015


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> 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 <mailto: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 <mailto: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 <mailto: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/ <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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> _______
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> Christian Jørgensen
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