[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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