FIST - missing torsional
Francesco
francesc... at gmail.com
Fri Jan 21 10:15:15 UTC 2011
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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