From 5b58cb736dd30f62432f040063bb13aa228ed7f4 Mon Sep 17 00:00:00 2001 From: Teodoro Laino Date: Sat, 12 May 2007 13:34:24 +0000 Subject: [PATCH] printing biased and weighting energy for alchemical change free energy calculations. 1 more regtest. svn-origin-rev: 6049 --- src/force_env_methods.F | 36 +++- src/fparser.F | 30 +-- src/input_cp2k_motion.F | 10 +- tests/FE/regtest-3/Solv_alch_chng.inp | 268 ++++++++++++++++++++++++++ tests/FE/regtest-3/TEST_FILES | 7 + tests/FE/regtest-3/TEST_FILES_RESET | 2 + tests/FE/regtest-3/ala_s.pdb | 13 ++ tests/FE/regtest-3/ala_s.pot | 113 +++++++++++ tests/FE/regtest-3/ala_s.psf | 49 +++++ tests/FE/regtest-3/ser_s.pdb | 14 ++ tests/FE/regtest-3/ser_s.pot | 128 ++++++++++++ tests/FE/regtest-3/ser_s.psf | 51 +++++ tests/FE/regtest-3/tidy | 18 ++ tests/TEST_DIRS | 1 + 14 files changed, 722 insertions(+), 18 deletions(-) create mode 100644 tests/FE/regtest-3/Solv_alch_chng.inp create mode 100644 tests/FE/regtest-3/TEST_FILES create mode 100644 tests/FE/regtest-3/TEST_FILES_RESET create mode 100644 tests/FE/regtest-3/ala_s.pdb create mode 100644 tests/FE/regtest-3/ala_s.pot create mode 100644 tests/FE/regtest-3/ala_s.psf create mode 100644 tests/FE/regtest-3/ser_s.pdb create mode 100644 tests/FE/regtest-3/ser_s.pot create mode 100644 tests/FE/regtest-3/ser_s.psf create mode 100644 tests/FE/regtest-3/tidy diff --git a/src/force_env_methods.F b/src/force_env_methods.F index 7048339093..311069336d 100644 --- a/src/force_env_methods.F +++ b/src/force_env_methods.F @@ -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)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,& diff --git a/src/fparser.F b/src/fparser.F index 98cffe9f04..b6a7cfd119 100644 --- a/src/fparser.F +++ b/src/fparser.F @@ -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) diff --git a/src/input_cp2k_motion.F b/src/input_cp2k_motion.F index 967b9c8936..f74025a677 100644 --- a/src/input_cp2k_motion.F +++ b/src/input_cp2k_motion.F @@ -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 diff --git a/tests/FE/regtest-3/Solv_alch_chng.inp b/tests/FE/regtest-3/Solv_alch_chng.inp new file mode 100644 index 0000000000..d536dbbbaf --- /dev/null +++ b/tests/FE/regtest-3/Solv_alch_chng.inp @@ -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 + diff --git a/tests/FE/regtest-3/TEST_FILES b/tests/FE/regtest-3/TEST_FILES new file mode 100644 index 0000000000..9ae70c2fc1 --- /dev/null +++ b/tests/FE/regtest-3/TEST_FILES @@ -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 diff --git a/tests/FE/regtest-3/TEST_FILES_RESET b/tests/FE/regtest-3/TEST_FILES_RESET new file mode 100644 index 0000000000..2b1ddefe12 --- /dev/null +++ b/tests/FE/regtest-3/TEST_FILES_RESET @@ -0,0 +1,2 @@ +# +# just add file names for which the reference needs to be reset below, with some comment diff --git a/tests/FE/regtest-3/ala_s.pdb b/tests/FE/regtest-3/ala_s.pdb new file mode 100644 index 0000000000..b92a70758d --- /dev/null +++ b/tests/FE/regtest-3/ala_s.pdb @@ -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 diff --git a/tests/FE/regtest-3/ala_s.pot b/tests/FE/regtest-3/ala_s.pot new file mode 100644 index 0000000000..940129ed67 --- /dev/null +++ b/tests/FE/regtest-3/ala_s.pot @@ -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 diff --git a/tests/FE/regtest-3/ala_s.psf b/tests/FE/regtest-3/ala_s.psf new file mode 100644 index 0000000000..b6361d0500 --- /dev/null +++ b/tests/FE/regtest-3/ala_s.psf @@ -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 + diff --git a/tests/FE/regtest-3/ser_s.pdb b/tests/FE/regtest-3/ser_s.pdb new file mode 100644 index 0000000000..160f154c52 --- /dev/null +++ b/tests/FE/regtest-3/ser_s.pdb @@ -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 diff --git a/tests/FE/regtest-3/ser_s.pot b/tests/FE/regtest-3/ser_s.pot new file mode 100644 index 0000000000..7e7461e795 --- /dev/null +++ b/tests/FE/regtest-3/ser_s.pot @@ -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 diff --git a/tests/FE/regtest-3/ser_s.psf b/tests/FE/regtest-3/ser_s.psf new file mode 100644 index 0000000000..2243571afc --- /dev/null +++ b/tests/FE/regtest-3/ser_s.psf @@ -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 + diff --git a/tests/FE/regtest-3/tidy b/tests/FE/regtest-3/tidy new file mode 100644 index 0000000000..8e44cbdbc5 --- /dev/null +++ b/tests/FE/regtest-3/tidy @@ -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 diff --git a/tests/TEST_DIRS b/tests/TEST_DIRS index 3b03864ca8..26bf6d3e1b 100644 --- a/tests/TEST_DIRS +++ b/tests/TEST_DIRS @@ -38,5 +38,6 @@ QS SE/regtest-2 Fist/regtest-2 SE/regtest +FE/regtest-3 FE/regtest-2 QS/regtest-ot-refine