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printing biased and weighting energy for alchemical change free energy calculations.

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1 more regtest.


svn-origin-rev: 6049
This commit is contained in:
Teodoro Laino 2007-05-12 13:34:24 +00:00
parent 44499ca64b
commit 5b58cb736d
14 changed files with 722 additions and 18 deletions
Download patch file Download diff file Expand all files Collapse all files

36
src/force_env_methods.F
View file

@ -1333,7 +1333,7 @@ SUBROUTINE mixed_energy_forces(force_env, need_f, error)
my_par(SIZE(variables)+1:) = parameters(1:SIZE(parameters))
my_val(SIZE(variables)+1:) = par_values(1:SIZE(parameters))
END IF
CALL initf(1)
CALL initf(2)
CALL parsef(1,TRIM(coupling_function),my_par)
! Now the hardest part.. map energy with corresponding force_eval
mixed_energy%pot= evalf(1,my_val)
@ -1414,13 +1414,18 @@ SUBROUTINE dump_der_par(my_val, my_par, dx, lerr, root_section, nforce_eval, err
CHARACTER(len=*), PARAMETER :: routineN = 'dump_der_par', &
routineP = moduleN//':'//routineN
CHARACTER(LEN=default_path_length) :: coupling_function
CHARACTER(LEN=default_string_length) :: par
INTEGER :: i, iforce_eval, output_unit
CHARACTER(LEN=default_string_length), &
DIMENSION(:), POINTER :: data_function
INTEGER :: i, iforce_eval, ipar, j, &
output_unit
LOGICAL :: explicit, failure
REAL(KIND=dp) :: dedf, err
REAL(KIND=dp) :: d_ene_w, dedf, ene_w, err
TYPE(cp_logger_type), POINTER :: logger
TYPE(section_vals_type), POINTER :: fe_section
NULLIFY(data_function)
failure = .FALSE.
logger => cp_error_get_logger(error)
fe_section => section_vals_get_subs_vals(root_section,&
@ -1432,9 +1437,26 @@ SUBROUTINE dump_der_par(my_val, my_par, dx, lerr, root_section, nforce_eval, err
IF (my_par(i)==par) EXIT
END DO
CPPrecondition(i<=SIZE(my_par),cp_failure_level,routineP,error,failure)
dedf = evalfd(1,i,my_val,dx,err)
ipar = i
dedf = evalfd(1,ipar,my_val,dx,err)
CPPostconditionNoFail(ABS(err)<lerr,cp_warning_level,routineP,error)
! We must print now the energy of the biased system, the weigthing energy
! and the derivative w.r.t.the coupling parameter of the biased energy
! Retrieve the expression of the weighting function:
CALL section_vals_val_get(fe_section,"WEIGHTING_FUNCTION",&
c_vals=data_function,error=error)
! Clean the function structure
coupling_function = ""
DO j = 1, SIZE(data_function)
coupling_function(LEN_TRIM(coupling_function)+1:) = TRIM(data_function(j))
END DO
CALL parsef(2,TRIM(coupling_function),my_par)
ene_w = evalf(2,my_val)
d_ene_w = evalfd(2,ipar,my_val,dx,err)
CPPostconditionNoFail(ABS(err)<lerr,cp_warning_level,routineP,error)
! Print info
output_unit = cp_print_key_unit_nr(logger,root_section,"MOTION%FREE_ENERGY%FREE_ENERGY_INFO",&
extension=".free_energy",error=error)
IF (output_unit>0) THEN
@ -1443,8 +1465,12 @@ SUBROUTINE dump_der_par(my_val, my_par, dx, lerr, root_section, nforce_eval, err
WRITE(output_unit,'(T2,"ALCHEMICAL CHANGE| FORCE_EVAL Nr.",I5,T48,"ENERGY (Hartree)= ",F15.9)')&
iforce_eval, my_val(iforce_eval)
END DO
WRITE(output_unit,'(T2,"ALCHEMICAL CHANGE| DERIVATIVE OF ENERGY w.r.t. PARAMETER (",A,")",T66,F15.9)')&
WRITE(output_unit,'(T2,"ALCHEMICAL CHANGE| DERIVATIVE OF TOTAL ENERGY [ PARAMETER (",A,") ]",T66,F15.9)')&
TRIM(par),dedf
WRITE(output_unit,'(T2,"ALCHEMICAL CHANGE| DERIVATIVE OF BIASED ENERGY [ PARAMETER (",A,") ]",T66,F15.9)')&
TRIM(par),dedf-d_ene_w
WRITE(output_unit,'(T2,"ALCHEMICAL CHANGE| BIASING UMBRELLA POTENTIAL ",T66,F15.9)')&
ene_w
WRITE(output_unit,'(T2,79("-"))')
END IF
CALL cp_print_key_finished_output(output_unit,logger,root_section,&

30
src/fparser.F
View file

@ -94,20 +94,26 @@ CONTAINS
INTEGER :: i, istat
!----- -------- --------- --------- --------- --------- --------- --------- -------
DO i = 1, SIZE(Comp)
DEALLOCATE ( Comp(i)%ByteCode, stat = istat)
IF (istat /= 0) THEN
WRITE(*,*) '*** Parser error: Memmory deallocation for byte code failed'
STOP
IF (ASSOCIATED(Comp(i)%ByteCode)) THEN
DEALLOCATE ( Comp(i)%ByteCode, stat = istat)
IF (istat /= 0) THEN
WRITE(*,*) '*** Parser error: Memmory deallocation for byte code failed'
STOP
END IF
END IF
DEALLOCATE ( Comp(i)%Immed, stat=istat)
IF (istat /= 0) THEN
WRITE(*,*) '*** Parser error: Memmory deallocation for Immed Size failed'
STOP
IF (ASSOCIATED(Comp(i)%Immed)) THEN
DEALLOCATE ( Comp(i)%Immed, stat=istat)
IF (istat /= 0) THEN
WRITE(*,*) '*** Parser error: Memmory deallocation for Immed Size failed'
STOP
END IF
END IF
DEALLOCATE ( Comp(i)%Stack, stat=istat)
IF (istat /= 0) THEN
WRITE(*,*) '*** Parser error: Memmory deallocation for Stack Size failed'
STOP
IF (ASSOCIATED(Comp(i)%Stack)) THEN
DEALLOCATE ( Comp(i)%Stack, stat=istat)
IF (istat /= 0) THEN
WRITE(*,*) '*** Parser error: Memmory deallocation for Stack Size failed'
STOP
END IF
END IF
END DO
DEALLOCATE ( Comp, stat=istat)

10
src/input_cp2k_motion.F
View file

@ -453,7 +453,15 @@ CONTAINS
usage="PARAMETERS k", required=.TRUE., type_of_var=char_t,&
n_var=1, error=error)
CALL section_add_keyword(section,keyword,error=error)
CALL keyword_release(keyword,error=error)
CALL keyword_release(keyword,error=error)
CALL keyword_create(keyword, name="WEIGHTING_FUNCTION",&
description="Specifies the weighting function (umbrella potential, part of the mixing function)",&
usage="WEIGHTING_FUNCTION (E1+E2-LOG(E1/E2))", type_of_var=char_t,&
n_var=-1, default_c_vals=(/"0"/),error=error)
CALL section_add_keyword(section,keyword,error=error)
CALL keyword_release(keyword,error=error)
END IF
END SUBROUTINE create_ac_section

268
tests/FE/regtest-3/Solv_alch_chng.inp Normal file
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@ -0,0 +1,268 @@
&MULTIPLE_FORCE_EVALS
FORCE_EVAL_ORDER 2 3 4 5
MULTIPLE_SUBSYS T
&END
&FORCE_EVAL
METHOD MIXED
&MIXED
MIXING_TYPE GENMIX
&GENERIC
MIXING_FUNCTION k*X+(1.0-k)*Y+(1.0-k)*Z+k*J
VARIABLES X Y Z J
PARAMETERS k
VALUES 0.5
&END
&MAPPING
&FORCE_EVAL_MIXED
&FRAGMENT 1
1 6
&END
&FRAGMENT 2
7 16
&END
&FRAGMENT 3
17 22
&END
&FRAGMENT 4
23 33
&END
&FRAGMENT 5
34 1851
&END
&END
&FORCE_EVAL 1
&FRAGMENT 1
1 6
MAP 1
&END
&FRAGMENT 2
7 16
MAP 2
&END
&FRAGMENT 3
17 22
MAP 3
&END
&FRAGMENT 4
23 1840
MAP 5
&END
&END
&FORCE_EVAL 2
&FRAGMENT 1
1 6
MAP 1
&END
&FRAGMENT 2
7 17
MAP 4
&END
&FRAGMENT 3
18 23
MAP 3
&END
&FRAGMENT 4
24 1841
MAP 5
&END
&END
&FORCE_EVAL 3
&FRAGMENT 1
1 11
MAP 4
&END
&END
&FORCE_EVAL 4
&FRAGMENT 1
1 10
MAP 2
&END
&END
&END
&END
&SUBSYS
&TOPOLOGY
CONNECTIVITY OFF
COORDINATE PDB
COORD_FILE_NAME ../regtest-1/full.pdb
&END TOPOLOGY
&CELL
ABC 30.9751780 30.8599250 30.7278700
UNIT ANGSTROM
&END CELL
&END SUBSYS
&END FORCE_EVAL
&FORCE_EVAL
METHOD FIST
&MM
&FORCEFIELD
PARM_FILE_NAME ../regtest-1/ala.pot
parmtype CHM
&SPLINE
EMAX_SPLINE 100000000.0
&END
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE spme
ALPHA .5
GMAX 36
O_SPLINE 6
&END EWALD
&END POISSON
&END MM
&SUBSYS
&TOPOLOGY
CONNECTIVITY PSF
CONN_FILE_NAME ../regtest-1/ala.psf
COORDINATE PDB
COORD_FILE_NAME ../regtest-1/ala.pdb
&END TOPOLOGY
&CELL
ABC 30.9751780 30.8599250 30.7278700
UNIT ANGSTROM
&END CELL
&END SUBSYS
&END FORCE_EVAL
&FORCE_EVAL
METHOD FIST
&MM
&FORCEFIELD
PARM_FILE_NAME ../regtest-1/ser.pot
parmtype CHM
&SPLINE
EMAX_SPLINE 100000000.0
&END
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE spme
ALPHA .5
GMAX 36
O_SPLINE 6
&END EWALD
&END POISSON
&END MM
&SUBSYS
&TOPOLOGY
CONNECTIVITY PSF
CONN_FILE_NAME ../regtest-1/ser.psf
COORDINATE PDB
COORD_FILE_NAME ../regtest-1/ser.pdb
&END TOPOLOGY
&CELL
ABC 30.9751780 30.8599250 30.7278700
UNIT ANGSTROM
&END CELL
&END SUBSYS
&END FORCE_EVAL
&FORCE_EVAL
METHOD FIST
&MM
&FORCEFIELD
NONBONDED F
NONBONDED14 F
PARM_FILE_NAME ser_s.pot
parmtype CHM
&SPLINE
EMAX_SPLINE 100000000.0
&END
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE none
&END EWALD
&END POISSON
&END MM
&SUBSYS
&TOPOLOGY
CONNECTIVITY PSF
CONN_FILE_NAME ser_s.psf
COORDINATE PDB
COORD_FILE_NAME ser_s.pdb
&END TOPOLOGY
&CELL
ABC 30.9751780 30.8599250 30.7278700
UNIT ANGSTROM
&END CELL
&END SUBSYS
&END FORCE_EVAL
&FORCE_EVAL
METHOD FIST
&MM
&FORCEFIELD
NONBONDED F
NONBONDED14 F
PARM_FILE_NAME ala_s.pot
parmtype CHM
&SPLINE
EMAX_SPLINE 100000000.0
&END
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE none
&END EWALD
&END POISSON
&END MM
&SUBSYS
&TOPOLOGY
CONNECTIVITY PSF
CONN_FILE_NAME ala_s.psf
COORDINATE PDB
COORD_FILE_NAME ala_s.pdb
&END TOPOLOGY
&CELL
ABC 30.9751780 30.8599250 30.7278700
UNIT ANGSTROM
&END CELL
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
FFTLIB FFTSG
PROJECT DDG_SOLVATION
RUN_TYPE MD
PRINT_LEVEL LOW
&END GLOBAL
&MOTION
&MD
ENSEMBLE NPT_I
STEPS 10
TIMESTEP 0.5
TEMPERATURE 200.0
&NOSE
LENGTH 3
YOSHIDA 3
TIMECON 300
MTS 2
&END NOSE
&PRINT
&ENERGY
EACH 1
&END
&END
PV_AVA
&END MD
&PRINT
&TRAJECTORY
EACH 100
&END
&VELOCITIES OFF
&END
&FORCES OFF
&END
&RESTART_HISTORY OFF
&END
&RESTART
EACH 10
&END
&END
&FREE_ENERGY
METHOD AC
&ALCHEMICAL_CHANGE
PARAMETER k
WEIGHTING_FUNCTION (1.0-k)*Z+k*J
&END
&END
&END MOTION

7
tests/FE/regtest-3/TEST_FILES Normal file
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@ -0,0 +1,7 @@
# runs are executed in the same order as in this file
# the second field tells which test should be run in order to compare with the last available output
# e.g. 0 means do not compare anything, running is enough
# 1 compares the last total energy in the file
# for details see cp2k/tools/do_regtest
#
Solv_alch_chng.inp 2

2
tests/FE/regtest-3/TEST_FILES_RESET Normal file
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@ -0,0 +1,2 @@
#
# just add file names for which the reference needs to be reset below, with some comment

13
tests/FE/regtest-3/ala_s.pdb Normal file
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@ -0,0 +1,13 @@
REMARK ALA
ATOM 1 N ALA 1 3.326 1.548 0.000 N
ATOM 2 H ALA 1 3.909 0.724 0.000 H
ATOM 3 CA ALA 1 3.970 2.846 0.000 C
ATOM 4 HA ALA 1 3.672 3.400 -0.890 H
ATOM 5 CB ALA 1 3.577 3.654 1.232 C
ATOM 6 1HB ALA 1 3.877 3.116 2.131 H
ATOM 7 2HB ALA 1 4.075 4.623 1.206 H
ATOM 8 3HB ALA 1 2.497 3.801 1.241 H
ATOM 9 C ALA 1 5.486 2.705 0.000 C
ATOM 10 O ALA 1 6.009 1.593 0.000 O
TER
END

113
tests/FE/regtest-3/ala_s.pot Normal file
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@ -0,0 +1,113 @@
*>>>>>>> AMBER FF Converted into CHARMM FF style <<<<<<<
*>>>>>>> Generated on :: 20070512 123039.991 +0100 by :: teo <<<<<<<
*>>>>>>> pcihpc07 <<<<<<<
*>>>>>>> Leap Title :: ALA <<<<<<<
*>>>>>>> Send all comments related to the FFs conversion to <<<<<<<
*>>>>>>> teodoro.laino@gmail.com <<<<<<<
BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb b0
!
N H 434.000000000 1.010000000
CT1 H1 340.000000000 1.090000000
CT2 HC 340.000000000 1.090000000
N CT1 337.000000000 1.449000000
CT1 CT2 310.000000000 1.526000000
CT1 C 317.000000000 1.522000000
C O 570.000000000 1.229000000
ANGLES
!
!V(angle) = Ktheta(Theta - Theta0)**2
!
!V(Urey-Bradley) = Kub(S - S0)**2
!
!Ktheta: kcal/mole/rad**2
!Theta0: degrees
!Kub: kcal/mole/A**2 (Urey-Bradley)
!S0: A
!
!atom types Ktheta Theta0 Kub S0
!
N CT1 H1 50.000000000 109.500046929
H N CT1 50.000000000 118.040050474
CT1 CT2 HC 50.000000000 109.500046929
H1 CT1 CT2 50.000000000 109.500046929
H1 CT1 C 50.000000000 109.500046929
HC CT2 HC 35.000000000 109.500046929
N CT1 CT2 80.000000000 109.700047015
N CT1 C 63.000000000 110.100047186
CT1 C O 80.000000000 120.400051601
CT2 CT1 C 63.000000000 111.100047615
DIHEDRALS
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!
!atom types Kchi n delta
!
N CT1 CT2 HC 0.155555556 3 0.000000000
H N CT1 H1 0.000000000 2 0.000000000
H N CT1 CT2 0.000000000 2 0.000000000
H N CT1 C 0.000000000 2 0.000000000
H1 CT1 CT2 HC 0.155555556 3 0.000000000
H1 CT1 C O 0.800000000 1 0.000000000
H1 CT1 C O 0.080000000 3 180.000077144
HC CT2 CT1 C 0.155555556 3 0.000000000
N CT1 C O 0.000000000 2 0.000000000
CT2 CT1 C O 0.000000000 2 0.000000000
IMPROPER
!
!V(improper) = Kpsi(psi - psi0)**2
!
!Kpsi: kcal/mole/rad**2
!psi0: degrees
!note that the second column of numbers (0) is ignored
!
!atom types Kpsi psi0
!
NONBONDED
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
!
N 0.000000000 0.170000000 1.824000000
H 0.000000000 0.015700000 0.600000000
CT1 0.000000000 0.109400000 1.908000000
H1 0.000000000 0.015700000 1.386999999
CT2 0.000000000 0.109400000 1.908000000
HC 0.000000000 0.015700000 1.487000000
C 0.000000000 0.086000000 1.908000000
O 0.000000000 0.210000000 1.661200000
END
!
! This Section can be cutted & pasted into the Fist input file..
!
CHARGES
N -0.493700000
H 0.301800000
CT1 0.044800000
H1 0.022800000
CT2 -0.090900000
HC 0.042500000
C 0.673099998
O -0.585399999
END CHARGES

49
tests/FE/regtest-3/ala_s.psf Normal file
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@ -0,0 +1,49 @@
PSF EXT
1 !NTITLE
Conversion from AMBER PARMTOP ::ALA
10 !NATOM
1 MOL01 1 ALA N N -0.493700 14.010 0
2 MOL01 1 ALA H H 0.301800 1.008 0
3 MOL01 1 ALA CA CT1 0.044800 12.010 0
4 MOL01 1 ALA HA H1 0.022800 1.008 0
5 MOL01 1 ALA CB CT2 -0.090900 12.010 0
6 MOL01 1 ALA HB1 HC 0.042500 1.008 0
7 MOL01 1 ALA HB2 HC 0.042500 1.008 0
8 MOL01 1 ALA HB3 HC 0.042500 1.008 0
9 MOL01 1 ALA C C 0.673100 12.010 0
10 MOL01 1 ALA O O -0.585400 16.000 0
9 !NBOND
1 2 3 4 5 6 5 7
5 8 1 3 3 5 3 9
9 10
14 !NTHETA
1 3 4 2 1 3 3 5 6
3 5 7 3 5 8 4 3 5
4 3 9 6 5 7 6 5 8
7 5 8 1 3 5 1 3 9
3 9 10 5 3 9
15 !NPHI
1 3 5 6 1 3 5 7
1 3 5 8 2 1 3 4
2 1 3 5 2 1 3 9
4 3 5 6 4 3 5 7
4 3 5 8 4 3 9 10
6 5 3 9 7 5 3 9
8 5 3 9 1 3 9 10
5 3 9 10
0 !NIMPHI
0 !NDON
0 !NACC
0 !NNB
0 !NGRP

14
tests/FE/regtest-3/ser_s.pdb Normal file
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@ -0,0 +1,14 @@
REMARK SER
ATOM 1 N SER 1 3.326 1.548 0.000 N
ATOM 2 H SER 1 3.909 0.724 0.000 H
ATOM 3 CA SER 1 3.970 2.846 0.000 C
ATOM 4 HA SER 1 3.672 3.400 -0.890 H
ATOM 5 CB SER 1 3.577 3.654 1.232 C
ATOM 6 2HB SER 1 2.497 3.801 1.241 H
ATOM 7 3HB SER 1 3.877 3.116 2.131 H
ATOM 8 OG SER 1 4.231 4.925 1.197 O
ATOM 9 HG SER 1 3.983 5.434 1.973 H
ATOM 10 C SER 1 5.486 2.705 0.000 C
ATOM 11 O SER 1 6.009 1.593 0.000 O
TER
END

128
tests/FE/regtest-3/ser_s.pot Normal file
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@ -0,0 +1,128 @@
*>>>>>>> AMBER FF Converted into CHARMM FF style <<<<<<<
*>>>>>>> Generated on :: 20070512 123045.978 +0100 by :: teo <<<<<<<
*>>>>>>> pcihpc07 <<<<<<<
*>>>>>>> Leap Title :: SER <<<<<<<
*>>>>>>> Send all comments related to the FFs conversion to <<<<<<<
*>>>>>>> teodoro.laino@gmail.com <<<<<<<
BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb b0
!
N H 434.000000000 1.010000000
CT1 H11 340.000000000 1.090000000
CT2 H12 340.000000000 1.090000000
OH HO 553.000000000 0.960000000
N CT1 337.000000000 1.449000000
CT1 CT2 310.000000000 1.526000000
CT1 C 317.000000000 1.522000000
CT2 OH 320.000000000 1.410000000
C O 570.000000000 1.229000000
ANGLES
!
!V(angle) = Ktheta(Theta - Theta0)**2
!
!V(Urey-Bradley) = Kub(S - S0)**2
!
!Ktheta: kcal/mole/rad**2
!Theta0: degrees
!Kub: kcal/mole/A**2 (Urey-Bradley)
!S0: A
!
!atom types Ktheta Theta0 Kub S0
!
N CT1 H11 50.000000000 109.500046929
H N CT1 50.000000000 118.040050474
CT1 CT2 H12 50.000000000 109.500046929
H11 CT1 CT2 50.000000000 109.500046929
H11 CT1 C 50.000000000 109.500046929
CT2 OH HO 55.000000000 108.500046500
H12 CT2 H12 35.000000000 109.500046929
H12 CT2 OH 50.000000000 109.500046929
N CT1 CT2 80.000000000 109.700047015
N CT1 C 63.000000000 110.100047186
CT1 CT2 OH 50.000000000 109.500046929
CT1 C O 80.000000000 120.400051601
CT2 CT1 C 63.000000000 111.100047615
DIHEDRALS
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!
!atom types Kchi n delta
!
N CT1 CT2 H12 0.155555556 3 0.000000000
H N CT1 H11 0.000000000 2 0.000000000
H N CT1 CT2 0.000000000 2 0.000000000
H N CT1 C 0.000000000 2 0.000000000
CT1 CT2 OH HO 0.250000000 1 0.000000000
CT1 CT2 OH HO 0.160000000 3 0.000000000
H11 CT1 CT2 H12 0.155555556 3 0.000000000
H11 CT1 CT2 OH 0.250000000 1 0.000000000
H11 CT1 C O 0.800000000 1 0.000000000
H11 CT1 C O 0.080000000 3 180.000077144
H12 CT2 CT1 C 0.155555556 3 0.000000000
H12 CT2 OH HO 0.166666667 3 0.000000000
N CT1 CT2 OH 0.155555556 3 0.000000000
N CT1 C O 0.000000000 2 0.000000000
CT2 CT1 C O 0.000000000 2 0.000000000
OH CT2 CT1 C 0.155555556 3 0.000000000
IMPROPER
!
!V(improper) = Kpsi(psi - psi0)**2
!
!Kpsi: kcal/mole/rad**2
!psi0: degrees
!note that the second column of numbers (0) is ignored
!
!atom types Kpsi psi0
!
NONBONDED
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
!
N 0.000000000 0.170000000 1.824000000
H 0.000000000 0.015700000 0.600000000
CT1 0.000000000 0.109400000 1.908000000
H11 0.000000000 0.015700000 1.386999999
CT2 0.000000000 0.109400000 1.908000000
H12 0.000000000 0.015700000 1.386999999
OH 0.000000000 0.210400000 1.721000000
HO 0.000000000 0.000000000 0.000000000
C 0.000000000 0.086000000 1.908000000
O 0.000000000 0.210000000 1.661200000
END
!
! This Section can be cutted & pasted into the Fist input file..
!
CHARGES
N -0.493700000
H 0.301800000
CT1 0.071700000
H11 0.016400000
CT2 0.134500000
H12 0.036100000
OH -0.559300001
HO 0.368700000
C 0.673099998
O -0.585399999
END CHARGES

51
tests/FE/regtest-3/ser_s.psf Normal file
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@ -0,0 +1,51 @@
PSF EXT
1 !NTITLE
Conversion from AMBER PARMTOP ::SER
11 !NATOM
1 MOL01 1 SER N N -0.493700 14.010 0
2 MOL01 1 SER H H 0.301800 1.008 0
3 MOL01 1 SER CA CT1 0.071700 12.010 0
4 MOL01 1 SER HA H11 0.016400 1.008 0
5 MOL01 1 SER CB CT2 0.134500 12.010 0
6 MOL01 1 SER HB2 H12 0.036100 1.008 0
7 MOL01 1 SER HB3 H12 0.036100 1.008 0
8 MOL01 1 SER OG OH -0.559300 16.000 0
9 MOL01 1 SER HG HO 0.368700 1.008 0
10 MOL01 1 SER C C 0.673100 12.010 0
11 MOL01 1 SER O O -0.585400 16.000 0
10 !NBOND
1 2 3 4 5 6 5 7
8 9 1 3 3 5 3 10
5 8 10 11
15 !NTHETA
1 3 4 2 1 3 3 5 6
3 5 7 4 3 5 4 3 10
5 8 9 6 5 7 6 5 8
7 5 8 1 3 5 1 3 10
3 5 8 3 10 11 5 3 10
18 !NPHI
1 3 5 6 1 3 5 7
2 1 3 4 2 1 3 5
2 1 3 10 3 5 8 9
4 3 5 6 4 3 5 7
4 3 5 8 4 3 10 11
6 5 3 10 6 5 8 9
7 5 3 10 7 5 8 9
1 3 5 8 1 3 10 11
5 3 10 11 8 5 3 10
0 !NIMPHI
0 !NDON
0 !NACC
0 !NNB
0 !NGRP

18
tests/FE/regtest-3/tidy Normal file
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@ -0,0 +1,18 @@
#!/bin/tcsh
# Script to clean files after execution of a test
echo "This script will clean the directory" $PWD "from scratch files.."
echo
foreach file (`cvs update -A -P|grep '? '|awk '{print $2}'`)
if ( ${file:e} == 'inp' ) then
echo "This files could be a new input file you don't want to be deleted.. Do you really want it deleted?"
if ( $1 == "-int" ) then
echo "You requested to run the cleaning script interactively! Forget about complains!"
rm -f $file
else
rm -i $file
endif
else
rm -f $file
endif
end
rm -f *.bak

1
tests/TEST_DIRS
View file

@ -38,5 +38,6 @@ QS
SE/regtest-2
Fist/regtest-2
SE/regtest
FE/regtest-3
FE/regtest-2
QS/regtest-ot-refine