PB-AM Examples ============== This is a few examples of input files and their expected outputs for each type of PB-AM run. The following runs are described in the previous section, and examples of their inputs and outputs follow: - :ref:`physlab` - :ref:`electlab` - :ref:`dynamlab` .. _physlab: Physical Calculation run ------------------------ Input Files ^^^^^^^^^^^ name: ``run.energyforce.inp`` .. code-block:: bash runtype energyforce runname energyforce.2sp.jmol.out units jmol salt 0.01 temp 353 idiel 4 sdiel 78 attypes 1 type 1 2 pqr 1 single_charge.pqr xyz 1 positions_2.xyz The files for PQR and XYZ are: name: ``single_charge.pqr`` .. code-block:: bash ATOM 1 N NTR 0 1.000 0.000 0.000 -1.0000 3.7300 ATOM 1 N NTR 0 0.000 1.000 0.000 -1.0000 6.3200 name: ``positions_2.xyz`` .. code-block:: bash -10.0 23.4 -8.7 0.0 0.0 -2.5 To run: .. code-block:: bash $$ ../../bin/pbam run.energyforce.inp Output Files ^^^^^^^^^^^^ And the resulting file: name: ``energyforce.2sp.jmol.out`` .. code-block:: bash My units are Joules/Mol MOLECULE #1 POSITION: [-10, 23.4, -8.7] ENERGY: 1328.86 FORCE: 1.19858e+08, [-36.6012 1.19858e+08 -1.65408e-05] TORQUE: 1.78426e+06, [1.28425 1.78426e+06 1.9978e-06] MOLECULE #2 POSITION: [0, 0, -2.5] ENERGY: 1328.86 FORCE: 1.19858e+08, [36.6012 -1.19858e+08 1.65408e-05] TORQUE: 1.78354e+06, [1.28372 1.78354e+06 1.99699e-06] .. _electlab: Electrostatics run ------------------ Input Files ^^^^^^^^^^^ name: ``run.electrostatic.inp`` .. code-block:: bash runtype electrostatics 140 runname electrostatic units kT salt 0.01 temp 298 idiel 4 sdiel 78 dx out.dx 3dmap electro_map.out gridct 2 grid2D 1 out.x.0.dat x 0 grid2D 2 out.x.-1.dat x -1 attypes 2 type 1 2 pqr 1 single_charge.pqr xyz 1 positions_2.xyz type 2 2 pqr 2 pos_charge.pqr xyz 2 positions_pos.xyz The files for PQR and XYZ files are: name: ``single_charge.pqr`` .. code-block:: bash ATOM 1 N NTR 0 0.000 1.000 0.000 4.0000 0.3200 ATOM 1 N NTR 0 0.000 0.000 -1.000 4.0000 0.3200 ATOM 1 X CEN 0 0.000 0.000 0.000 0.0000 2.0000 name: ``positions_2.xyz`` .. code-block:: bash 0.0 0.0 -5.0 0.0 0.0 5.0 name: ``pos_charge.pqr`` .. code-block:: bash ATOM 1 N NTR 0 0.000 1.000 0.000 -4.0000 0.3200 ATOM 1 N NTR 0 0.000 0.000 -1.000 -4.0000 0.3200 ATOM 1 X CEN 0 0.000 0.000 0.000 0.0000 2.0000 name: ``positions_pos.xyz`` .. code-block:: bash 0.0 5.0 0.0 0.0 -5.0 0.0 To run: .. code-block:: bash $$ ../../bin/pbam run.electrostatic.inp Output Files ^^^^^^^^^^^^ And the resulting files: name: ``out.dx`` .. code-block:: bash # Data from PBAM Electrostat run # My runname is out.dx and units kT/e object 1 class gridpositions counts 140 140 140 origin -4 -9 -9 delta 0.0571429 0.0e+00 0.0e+00 delta 0.0e00 0.128571 0.0e+00 delta 0.0e00 0.0e+00 0.128571 object 2 class gridconnections counts 140 140 140 object 3 class array type double rank 0 items 2744000 data follows 2.7203115e-01 3.0271755e-01 3.3459723e-01 3.6769040e-01 4.0201595e-01 4.3759129e-01 ..... -1.3185519e-01 -1.5849252e-01 -1.8359631e-01 -2.0722087e-01 -2.2942006e-01 -2.5024714e-01 -2.6975467e-01 -2.8799442e-01 attribute "dep" string "positions" object "regular positions regular connections" class field component "positions" value 1 component "connections" value 2 component "data" value 3 name: ``electro_map.out`` .. code-block:: bash # Data from PBAM Electrostat run # My runname is electro_map.out and units kT/e grid 10 10 10 origin -4 -9 -9 delta 0.8 1.8 1.8 0.00825 0.00006 -2.90002 -5.899956 0.00822 0.00071 -2.90002 -5.902602 name: ``out.x.0.dat`` .. code-block:: bash # Data from PBAM Electrostat run # My runname is out.x.0.dat units kT grid 140 140 axis x 0 origin -9 -9 delta 0.128571 0.128571 maxmin 39.23 -39.23 0.3605004 0.4030045 0.4474874 0.4940082 0.5426260 0.5933995 .. _dynamlab: Dynamics run ------------ Input Files ^^^^^^^^^^^ name: ``run.dynamics.inp`` .. code-block:: bash runtype dynamics 2 runname dyn_cont_barn salt 0.01 temp 298 idiel 4 sdiel 78 termct 1 termcombine or term 1 contact 2.5 1 2 attypes 2 type 1 2 move 0.015 0.000045 pqr 1 1BRS_chainA.pqr xyz 1 1 pos_1_1.xyz xyz 1 2 pos_1_2.xyz type 2 2 move 0.015 0.000045 pqr 2 1BRS_chainD.pqr xyz 2 1 pos_2_1.xyz xyz 2 2 pos_2_2.xyz The files for PQR (first 5 lines) and XYZ files for the first trajectories are: name: ``1BRS_chainA.pqr`` .. code-block:: bash ATOM 1700 N ALA B 1 20.757 52.394 30.692 0.1414 1.8240 ATOM 1702 CA ALA B 1 20.602 52.680 29.268 0.0962 1.9080 ATOM 1703 C ALA B 1 19.286 52.138 28.675 0.6163 1.9080 ATOM 1704 O ALA B 1 18.578 51.351 29.318 -0.5722 1.6612 ATOM 1705 CB ALA B 1 21.739 52.033 28.476 -0.0597 1.9080 name: ``pos_1_1.xyz`` .. code-block:: bash 61.25 61.25 61.25 -26.25 61.25 -26.25 name: ``1BRS_chainD.pqr`` .. code-block:: bash ATOM 1 N LYS D 1 48.330 40.393 9.798 0.0966 1.8240 ATOM 2 CA LYS D 1 47.401 39.287 9.370 -0.0015 1.9080 ATOM 3 C LYS D 1 47.507 38.911 7.890 0.7214 1.9080 ATOM 4 O LYS D 1 47.126 39.582 6.905 -0.6013 1.6612 ATOM 5 CB LYS D 1 45.995 39.632 9.817 0.0212 1.9080 name: ``pos_2_1.xyz`` .. code-block:: bash -26.25 61.25 61.25 61.25 -26.25 61.25 To run: .. code-block:: bash $$ ../../bin/pbam run.dynamics.inp Output Files ^^^^^^^^^^^^ And the resulting files: name: ``dyn_cont_barn_[traj#].xyz`` VMD readable XYZ file that shows the trajectory of molecules in the system. The time that is snapshot was printed from is given on the same line as the word Atom. The atoms of your input file are currently labeled N, and the coarse-grain center is labeled "X" in the first column of the XYZ file. .. code-block:: bash 3135 Atoms. Timestep (ps): 0 N -7.241 -0.530 18.703 N -6.015 -0.503 17.910 N -5.784 0.840 17.188 N -6.682 1.690 17.128 N -6.066 -1.580 16.827 N -7.519 -1.481 18.863 N -7.084 -0.079 19.584 name: ``dyn_cont_barn_[traj\#].dat`` Statistics from simulation printed out at the same time as each XYZ snapshot. The energy is not computed and should be ignored. .. code-block:: bash My units are Internal. Time (ps) 500.4 MOLECULE #1 POSITION: [0, 0, 0] ENERGY: 0 FORCE: 3.39124e-06, [1.69863e-06 2.07547e-06 6.5356e-07] TORQUE: 2.55224e-05, [-2.11728e-05 1.00774e-05 3.08631e-05] MOLECULE #2 POSITION: [87.211, 43.861, 21.691] ENERGY: 0 FORCE: 3.65373e-06, [-1.87502e-06 -2.21744e-06 -7.27314e-07] TORQUE: 1.91656e-05, [8.14396e-06 -1.22678e-05 1.56284e-05] name: ``dyn_nam_barn.stat`` Details about how each simulation has terminated and the time at which this occurred. .. code-block:: bash Molecule type 1 has fulfilled condition: r >= 500.00; at time (ps) 1.32367e+06 Molecule type 1 has fulfilled condition: r >= 500.00; at time (ps) 1.15712e+06 System has fulfilled condition: Type 0 and Type 1 are within 2.50; at time (ps) 1.90603e+06 Molecule type 1 has fulfilled condition: r >= 500.00; at time (ps) 2.18533e+06 System has fulfilled condition: Type 0 and Type 1 are within 2.50; at time (ps) 1.59066e+06