<https://lh3.googleusercontent.com/-dyTmC1pMzY0/WjexEXeyflI/AAAAAAAADfA/-imk0ASHQYkR4Oi3byRMlJUFcoRZA1fGQCLcBGAs/s1600/.png>
<https://lh3.googleusercontent.com/-NEGCu6ANRYs/WjexBaiZkSI/AAAAAAAADe8/pnQvzWDI8q45VJ6yYnXKbCMYXoVsgVuMQCLcBGAs/s1600/cp2k11.png>
Hi CP2K group,
I am trying to create a PSF file for ALOOH surface. I have a particular
requirement that the psf file should have connections shown as in left
figure.
I have created the PSF file, but CP2K shows error:
CP2K requires molecules to be contiguous and we have detected a non *
* [ABORT] contiguous one!! In particular a molecule defined from index
( *
* \___/ 1) to ( 210) contains other molecules, not connected!
My PSF file look like this:
256 !NATOM
1 14 01 DIAS Al1 YA 0.000000 0.0000 0
2 14 01 DIAS Al2 YA 0.000000 0.0000 0
3 03 01 DIAS Al3 YA 0.000000 0.0000 0
4 03 01 DIAS Al4 YA 0.000000 0.0000 0
5 13 01 DIAS Al5 YA 0.000000 0.0000 0
6 13 01 DIAS Al6 YA 0.000000 0.0000 0
7 02 01 DIAS Al7 YA 0.000000 0.0000 0
8 02 01 DIAS Al8 YA 0.000000 0.0000 0
9 12 01 DIAS Al9 YA 0.000000 0.0000 0
10 12 01 DIAS Al1A YA 0.000000 0.0000 0
11 01 01 DIAS Al1B YA 0.000000 0.0000 0
Questions:
1) If it is same molecule, then in PSF file should SEGMENT ID should be
defined exactly in a row? for instance
which format is correct for CP2K. See SEGMENT ID (second column).. Should
each molecule be defined in a row or it can be expressed randomly?
256 !NATOM
1 AA 01 DIAS Al1 YA 0.000000 0.0000 0
2 BB 01 DIAS Al4 YA 0.000000 0.0000 0
3 AA 01 DIAS Al3 YA 0.000000 0.0000 0
4 AA 01 DIAS Al2 YA 0.000000 0.0000 0
5 BB 01 DIAS Al5 YA 0.000000 0.0000 0
256 !NATOM
1 AA 01 DIAS Al1 YA 0.000000 0.0000 0
2 AA 01 DIAS Al2 YA 0.000000 0.0000 0
3 AA 01 DIAS Al3 YA 0.000000 0.0000 0
4 BB 01 DIAS Al4 YA 0.000000 0.0000 0
5 BB 01 DIAS Al5 YA 0.000000 0.0000 0
2) In my current ALO(OH), except for the non-hydroxy oxygen everything are
connected. I could create PSF connecting all atoms (easier to create for me
compared to the PSF separating the non-hydroxy oxygen). Is there any easier
way to define non-hydroxy oxygens as separate molecules, so that I can have
1-3 VdW, EI.
Please let me know. Attached are my PSF, input and PDB files.
On Saturday, February 14, 2015 at 2:53:48 PM UTC+1, Luca wrote:
>
> Hi Christian,
> I have investigated in your problem,
> Maybe the solution is in the definition of molecule
> in the PSF file . I have just reproduced your error using a small
> system.
> The original PSF created with psfgen for 10 waters and 2 ions (SOD and
> CLA) does not work in cp2k as it is.
>
> 29 !NATOM
> [..]
> 26 W1 9 TIP3 H1 HT 0.417000 1.0080 0
> 27 W1 9 TIP3 H2 HT 0.417000 1.0080 0
> 28 O1 10 CLA CLA CLA -1.000000 35.4500 0
> 29 O1 11 SOD SOD SOD 1.000000 22.9898 0
> [..]
>
> Because, cp2k read info about the molecule from segment definition the
> error arises from the fact that CLA and SOD have same fragment/segment
> name, which is "O1".
> If you change this name in the PSF file, it should be work.
>
> 28 O1 10 CLA CLA CLA -1.000000 35.4500 0
> 29 O2 11 SOD SOD SOD 1.000000 22.9898 0
>
> Good luck,
>
> Luca
>
>
>
>
> > My apologies. I've reported it now.
> >
> >
> > On 12 Feb 2015 21:47, "Teodoro Laino" <teod... at gmail.com <javascript:>>
> 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
> > > <chr... at gmail.com <javascript:>> 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
> > > <teod... at gmail.com <javascript:>> wrote:
> > > report this to the proper mailing list.
> > >
> > > > On 11 Feb 2015, at 23:04, Christian Jorgensen
> > > > <chr... at gmail.com <javascript:>> 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 <chr... at gmail.com <javascript:>> 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"
> > > > <teod... at gmail.com <javascript:>> 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
> > > > > <chr... at gmail.com <javascript:>>
> 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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