[CP2K:6143] Topology error QMMM or MM
Christian Jorgensen
chri... at gmail.com
Wed Feb 11 22:04:10 UTC 2015
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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