[CP2K:3063] Re: FIST - missing torsional

Teodoro Laino teodor... at gmail.com
Fri Jan 21 14:31:10 UTC 2011


you need to specify nonbonded_14 as well.
The number printed at the beginning is the whole number - the one really used is screened later on during the calculation.

Teo

On Jan 21, 2011, at 11:15 AM, Francesco wrote:

> Hi,
> 
> thanks Teo for the fast reply!
> 
> I have other questions related to this:
> 
> even if I activate the keywords EXCLUDE_VDW and EXLUDE_EI and I set
> them to 1-4 (instead of the default 1-3), the number of the calculated
> 1-4 interaction remains the same:
> 
> "GENERATE|  Number of 1-4 interactions
> generated:                             21"
> 
> With the same input, I still missing some parameters, that I cannot
> really understand: it is the same even if I use the keyword
> UNIQUE_SPLINE T
> 
> "FORCEFIELD| Missing Spline_Bond_Env   (   C,   C)"
> 
> 
> Attached the updated input file
> 
> Best regards,
> Francesco
> 
> 
> ------------------- INPUT ---------------------------
> 
> &FORCE_EVAL
>  METHOD FIST
>  &MM
>    &FORCEFIELD
>      &SPLINE
>        EMAX_SPLINE 10.00000000E-01
>      &END SPLINE
>      &BOND
>        ATOMS C C
>        K 0.05
>        R0 [angstrom] 1.390
>      &END BOND
>      &BOND
>        ATOMS C H
>        K 0.05
>        R0 [angstrom] 1.080
>      &END BOND
>      &BEND
>        ATOMS C C C
>        K [rad^-2kjmol] 376.6
>        THETA0 [deg] 120.0
>      &END BEND
>      &BEND
>        ATOMS C C H
>        K [rad^-2kjmol] 418.8
>        THETA0 [deg] 120.0
>      &END BEND
>      &TORSION
>        ATOMS C C C C
>        K 0.064
>        M 2
>        KIND CHARMM
>        PHI0 [deg] 180.0
>      &END TORSION
>      &TORSION
>        ATOMS C C C H
>        K 0.064
>        M 2
>        KIND CHARMM
>        PHI0 [deg] 180.0
>      &END TORSION
>      &TORSION
>        ATOMS H C C H
>        K 0.064
>        M 2
>        KIND CHARMM
>        PHI0 [deg] 180.0
>      &END TORSION
>      &IMPROPER
>        ATOMS C C C H
>        K 0.064
>        KIND CHARMM
>        PHI0 0.0
>      &END IMPROPER
>      &CHARGE
>        ATOM C
>        CHARGE -0.115
>      &END CHARGE
>      &CHARGE
>        ATOM H
>        CHARGE 0.115
>      &END CHARGE
>      &NONBONDED
>        &LENNARD-JONES
>          ATOMS C C
>          EPSILON [kjmol] 0.294
>          SIGMA [angstrom] 3.35
>          RCUT [angstrom] 11.0
>        &END LENNARD-JONES
>        &LENNARD-JONES
>          ATOMS H H
>          EPSILON [kjmol] 0.126
>          SIGMA [angstrom] 2.42
>          RCUT [angstrom] 11.0
>        &END LENNARD-JONES
>        &LENNARD-JONES
>          ATOMS C H
>          EPSILON [kjmol] 0.289
>          SIGMA [angstrom] 1.92
>          RCUT [angstrom] 11.0
>        &END LENNARD-JONES
>      &END NONBONDED
>    &END FORCEFIELD
>    &POISSON
>      POISSON_SOLVER ANALYTIC
>      PERIODIC NONE
>      &EWALD
>        EWALD_TYPE NONE
>        ALPHA .44
>        GMAX 21
>      &END EWALD
>    &END POISSON
>  &END MM
>  &SUBSYS
>    &CELL
>      PERIODIC NONE
>      ABC 20.0 20.0 20.0
>    &END CELL
>    &COORD
>  C      0.000000    0.000000    1.390000     1BEN
>  C      1.203775    0.000000    0.695000     1BEN
>  C      1.203775    0.000000   -0.695000     1BEN
>  C      0.000000    0.000000   -1.390000     1BEN
>  C     -1.203775    0.000000   -0.695000     1BEN
>  C     -1.203775    0.000000    0.695000     1BEN
>  H      0.000000    0.000000    2.470000     1BEN
>  H      2.139083    0.000000    1.235000     1BEN
>  H      2.139083    0.000000   -1.235000     1BEN
>  H      0.000000    0.000000   -2.470000     1BEN
>  H     -2.139083    0.000000   -1.235000     1BEN
>  H     -2.139083    0.000000    1.235000     1BEN
>    &END COORD
>    &TOPOLOGY
>      &CENTER_COORDINATES T
>      &END CENTER_COORDINATES
>      CONN_FILE_FORMAT GENERATE
>      EXCLUDE_EI 1-4
>      EXCLUDE_VDW 1-4
>    &END TOPOLOGY
>  &END SUBSYS
> &END FORCE_EVAL
> &GLOBAL
>  PRINT_LEVEL HIGH
>  PROJECT test2
>  RUN_TYPE WFN_OPT
> &END GLOBAL
> 
> 
> On Jan 21, 12:18 am, Teodoro Laino <teodor... at gmail.com> wrote:
>> hi Francesco,
>> 
>> indeed there was a bug when printing the atomic species of the missing parameter. It is now fixed in the CVS and FYI there are still parameters missing:
>> 
>>  FORCEFIELD| Missing Urey-Bradley      (   C,   C,   C)                        
>>  FORCEFIELD| Missing Urey-Bradley      (   C,   C,   H)                        
>> 
>>  FORCEFIELD| Missing Torsion           (   C,   C,   C,   H)                    
>>  FORCEFIELD| Missing Torsion           (   H,   C,   C,   H)                    
>>  FORCEFIELD| Missing Out of plane bend (   C,   H,   C,   C)    
>> 
>> you can safely ignore the UB (unless your pot includes them) but the two torsions and the out-of-plane bending maybe not (depends how you setup the improper actually..) ..
>> Cheers
>> Teo
>> 
>> On Jan 20, 2011, at 6:43 PM, Francesco wrote:
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>>> Hi,
>> 
>>> trying to simulate with FIST a molecule of benzene writing the
>>> forcefield directly in the input (attached below), even if I put the
>>> shell
>> 
>>> &TORSION
>>>   ATOMS C C C C
>>>   K 0.064
>>>   M 3
>>>   KIND CHARMM
>>>   PHI0 [deg] 180.0
>>> &END TORSION
>> 
>>> printing at HIGH output level, I have noticed
>> 
>>> FORCEFIELD| Missing Torsion           (   C,   C,   C,   C)
>> 
>>> Is it an issue?
>> 
>>> Thanks in advance,
>>> Francesco
>> 
>>> CP2K version 2.2.98 (Development Version)
>> 
>>> ---------------- INPUT -------------------
>> 
>>> &FORCE_EVAL
>>>  METHOD FIST
>>>  &MM
>>>    &FORCEFIELD
>>>      &SPLINE
>>>        EMAX_SPLINE 5.00000000E-01
>>>      &END SPLINE
>>>      &BOND
>>>        ATOMS C C
>>>        K 0.05
>>>        R0 [angstrom] 1.390
>>>      &END BOND
>>>      &BOND
>>>        ATOMS C H
>>>        K 0.05
>>>        R0 [angstrom] 1.080
>>>      &END BOND
>>>      &BEND
>>>        ATOMS C C C
>>>        K [rad^-2kjmol] 376.6
>>>        THETA0 [deg] 120.0
>>>      &END BEND
>>>      &BEND
>>>        ATOMS C C H
>>>        K [rad^-2kjmol] 418.8
>>>        THETA0 [deg] 120.0
>>>      &END BEND
>>>      &TORSION
>>>        ATOMS C C C C
>>>        K 0.064
>>>        M 3
>>>        KIND CHARMM
>>>        PHI0 [deg] 180.0
>>>      &END TORSION
>>>      &IMPROPER
>>>        ATOMS C C C H
>>>        K 0.064
>>>        KIND CHARMM
>>>        PHI0 0.0
>>>      &END IMPROPER
>>>      &CHARGE
>>>        ATOM C
>>>        CHARGE -0.115
>>>      &END CHARGE
>>>      &CHARGE
>>>        ATOM H
>>>        CHARGE 0.115
>>>      &END CHARGE
>>>      &NONBONDED
>>>        &LENNARD-JONES
>>>          ATOMS C C
>>>          EPSILON [kjmol] 0.294
>>>          SIGMA [angstrom] 3.35
>>>          RCUT [angstrom] 11.0
>>>        &END LENNARD-JONES
>>>        &LENNARD-JONES
>>>          ATOMS H H
>>>          EPSILON [kjmol] 0.126
>>>          SIGMA [angstrom] 2.42
>>>          RCUT [angstrom] 11.0
>>>        &END LENNARD-JONES
>>>        &LENNARD-JONES
>>>          ATOMS C H
>>>          EPSILON [kjmol] 0.289
>>>          SIGMA [angstrom] 1.92
>>>          RCUT [angstrom] 11.0
>>>        &END LENNARD-JONES
>>>      &END NONBONDED
>>>    &END FORCEFIELD
>>>    &POISSON
>>>      POISSON_SOLVER ANALYTIC
>>>      PERIODIC NONE
>>>      &EWALD
>>>        EWALD_TYPE NONE
>>>        ALPHA .44
>>>        GMAX 21
>>>      &END EWALD
>>>    &END POISSON
>>>  &END MM
>>>  &SUBSYS
>>>    &CELL
>>>      PERIODIC NONE
>>>      ABC 20.0 20.0 20.0
>>>    &END CELL
>>>    &COORD
>>>  C      0.000000    0.000000    1.390000     1BEN
>>>  C      1.203775    0.000000    0.695000     1BEN
>>>  C      1.203775    0.000000   -0.695000     1BEN
>>>  C      0.000000    0.000000   -1.390000     1BEN
>>>  C     -1.203775    0.000000   -0.695000     1BEN
>>>  C     -1.203775    0.000000    0.695000     1BEN
>>>  H      0.000000    0.000000    2.470000     1BEN
>>>  H      2.139083    0.000000    1.235000     1BEN
>>>  H      2.139083    0.000000   -1.235000     1BEN
>>>  H      0.000000    0.000000   -2.470000     1BEN
>>>  H     -2.139083    0.000000   -1.235000     1BEN
>>>  H     -2.139083    0.000000    1.235000     1BEN
>>>    &END COORD
>>>    &TOPOLOGY
>>>      &CENTER_COORDINATES T
>>>      &END CENTER_COORDINATES
>>>      CONN_FILE_FORMAT GENERATE
>>>    &END TOPOLOGY
>>>  &END SUBSYS
>>> &END FORCE_EVAL
>>> &GLOBAL
>>>  PRINT_LEVEL HIGH
>>>  PROJECT test2
>>>  RUN_TYPE WFN_OPT
>>> &END GLOBAL
>> 
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