PB-SAM Examples ================== This is a few examples of input files and their expected outputs for each type of PB-SAM run. Like PB-AM runs can be one of three options: - :ref:`pbsam_enfo` - :ref:`pbsam_elec` - :ref:`pbsam_dyn` Because PB-SAM is a bit more theoretically involved than PB-AM, it is time saving to save some files with program intermediates that can be later used as program inputs. They are described in the following section. PB-SAM intermediates --------------------- When running PB-SAM, a few intermediate quantities are generated and saved to files. These include - :ref:`pqrlab` - :ref:`imatlab` - :ref:`explab` .. _pqrlab: Coarse-Grain PQR files ^^^^^^^^^^^^^^^^^^^^^^^ The program uses the vertex file output from MSMS to coarse-grain the system. If the input file does not contain any CG centers (indicated by ``CEN`` keyword in the PQR file, then the MC CG process is run, and the output is stored to a file called ``[pqr input]_cg.pqr``, where ``[pqr input]`` is the input file name with the last four characters removed (presumably '.pqr'). .. code-block:: bash pqr 1 barnase.pqr surf 1 barnase.vert **Later use:** If you wish to run the system again, you can change the filename of the PQR file from the original to the new ``[pqr]_cg.pqr``, and the CG process will be skipped. .. code-block:: bash pqr 1 barnase_cg.pqr # _cg file has replaced pqr #surf 1 barnase.vert # commented out, no longer needed .. _imatlab: Imat: Surface integral files ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ After the system has been coarse-grained, surface integral matrices are generated for each CG sphere. These are binary files, and will be named as follows: ``[pqr input]sph[#].bin``, where like the CG output file, the pqr input has removed the last four characters, and the ``#`` indicating the number of the sphere within the molecule (zero-based). **Later use:** If you wish to run the system again, you can add the flag ``imat`` into the input file, with the prefix ``[pqr input]sph`` for the molecule. The program will append the sphere numbers after the ``sph``. Input file invocation is given below. Please note that if system conditions (dielectric constants, temperature, salt concentration) are changed, the ``imat`` files do not need to be regenerated. .. code-block:: bash pqr 1 barnase.pqr imat 1 barnasesph .. _explab: Exp: Expansion files ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ After the system has been coarse-grained and surface integral generated, the program will then perform a self-polarization for each molecule type designated in the input. Once the self-polarization has completed, the multipole expansions **H** and **F** representing the effective charge distribution on the molecular surface are printed to files, called: ``[pqr input].H.[#].exp`` and ``[pqr input].F.[#].exp``. where like the CG output file, the pqr input has removed the last four characters, and the ``#`` indicating the number of the sphere within the molecule (zero-based). **Later use:** If you wish to run the system again, you can add the flag ``exp`` into the input file, with the prefix ``[pqr input]`` for the molecule. The program will append letter H or F and the sphere numbers. Please note that if system conditions (dielectric constants, temperature, salt concentration) are changed, the ``exp`` files should be regenerated. .. code-block:: bash pqr 1 barnase.pqr exp 1 barnase .. _pbsam_enfo: Physical Calculation run ------------------------ Input Files ^^^^^^^^^^^ name: ``run.energyforce.inp`` .. code-block:: bash runtype energyforce runname gly_0.05M.out units kT salt 0.05 temp 298.15 idiel 4 sdiel 80 attypes 1 type 1 2 tolsp 2.0 surf 1 gly.vert #comment when system is CGed #imat 1 glyph #uncomment when system has been run once #exp 1 gly #uncomment when system has been run once pqr 1 gly.pqr xyz 1 zero.xyz The files for PQR, Surf, and XYZ are: name: ``gly.pqr`` ( the first few lines) .. code-block:: bash ATOM 1 C A 0 0.0000 0.0000 0.0000 -0.1550 1.8700 ATOM 2 C A 0 1.5000 0.0000 0.0000 0.6500 1.8700 ATOM 3 O A 0 2.1870 0.9730 0.0000 -0.5330 1.7600 ATOM 4 O A 0 1.9820 -1.2390 0.0110 -0.4280 1.5200 ATOM 5 C A 0 3.3800 -1.4580 0.0810 0.1240 1.8700 ATOM 6 C A 0 3.8360 -1.6880 1.5170 0.1220 1.8700 ATOM 7 C A 0 5.1860 -2.3750 1.5470 0.1430 1.8700 ATOM 8 O A 0 5.4810 -2.6680 2.9010 -0.4260 1.5200 ATOM 9 C A 0 6.6410 -3.2580 3.1620 0.6450 1.8700 ATOM 10 C A 0 6.8260 -3.4910 4.6340 -0.1550 1.8700 name: ``gly.vert`` ( the first few lines) .. code-block:: bash # MSMS solvent excluded surface vertices for gly.xyzr #vertex #sphere density probe_r 642 29 3.00 1.50 -0.041 -1.794 -0.525 -0.022 -0.960 -0.280 0 1 2 -0.248 -1.747 -0.847 0.116 -0.991 -0.065 0 16 2 0.947 -2.243 -0.470 -0.681 -0.661 -0.317 0 4 2 0.101 -0.896 -1.738 0.433 -0.217 -0.875 0 16 2 0.416 -0.678 -1.692 0.223 -0.362 -0.905 0 1 2 1.084 -0.678 -1.692 -0.223 -0.362 -0.905 0 2 2 1.084 0.906 -1.582 -0.223 0.485 -0.846 0 2 2 name: ``zero.xyz`` .. code-block:: bash 0.0 0.0 0.0 12.0 12.0 12.0 To run: .. code-block:: bash $$ ../../bin/pbsam run.energyforce.inp Output Files ^^^^^^^^^^^^ And the resulting file: name: ``gly_0.05M.out`` .. code-block:: bash My units are kT. Time: 0 Molecule #1 POSITION: [0, 0, 0] ENERGY: 6.17661e-05 FORCE: 0.00072349, [-0.000537635 -0.000423847 -0.000233967] TORQUE: 2.03503e-06, [-4.31343e-05 -0.000822915 0.00078854] Molecule #2 POSITION: [12, 12, 12] ENERGY: 6.21059e-05 FORCE: 0.000737173, [0.000535151 0.000445966 0.000241146] TORQUE: 8.2822e-06, [0.00196746 0.00132961 -0.00398844] .. _pbsam_elec: Electrostatics run ------------------ Input Files ^^^^^^^^^^^ name: ``run.electrostatic.inp`` .. code-block:: bash runtype electrostatics 150 runname barnase.out units kT salt 0.01 temp 298 idiel 2 sdiel 78 dx barnase.dx 3dmap barnase_map.out gridct 2 grid2D 1 barnase.y.0.dat y 0 grid2D 2 barnase.z.0.dat z 0 attypes 1 type 1 1 pqr 1 barnase.pqr surf 1 barnase.vert #pqr 1 barnase_cg.pqr #For when CG process is done #imat 1 barnasesph #For when imat calculation is done #exp 1 barnase #For when self-polarization is done xyz 1 zero.xyz The files for PQR, Surf, and XYZ files are: name: ``barnase.pqr`` ( the first few lines) .. 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: ``barnase.vert`` ( the first few lines) .. code-block:: bash # MSMS solvent excluded surface vertices for barnase.xyzr #vertex #sphere density probe_r 5720 878 1.00 1.50 5.097 50.485 18.262 0.322 -0.456 0.830 0 123 2 5.549 50.063 18.030 0.021 -0.174 0.984 0 121 2 6.503 50.902 19.073 -0.615 -0.734 0.289 0 133 2 5.437 49.956 18.007 -0.035 -0.228 0.973 0 121 2 4.986 50.378 18.239 0.266 -0.509 0.818 0 123 2 5.273 49.355 17.993 0.074 0.173 0.982 0 122 2 3.731 49.067 15.692 -0.890 -0.007 -0.457 0 122 2 name: ``zero.xyz`` .. code-block:: bash 0.0 0.0 0.0 To run: .. code-block:: bash $$ ../../bin/pbsam run.electrostatic.inp Output Files ^^^^^^^^^^^^ And the resulting files: name: ``barnase.dx`` .. code-block:: bash # Data from PBSAM Electrostat run # My runname is barnase.dx and units kT/e object 1 class gridpositions counts 100 100 100 origin -25.025 -24.4258 -30.4642 delta 0.538326 0.0e+00 0.0e+00 delta 0.0e00 0.493468 0.0e+00 delta 0.0e00 0.0e+00 0.563884 object 2 class gridconnections counts 100 100 100 object 3 class array type double rank 0 items 1000000 data follows 0.003659521 0.003697636 0.003732662 0.003764229 0.003791946 0.003815395 0.003834137 0.003847709 0.003855628 0.003857388 0.003852465 0.003840319 0.003820396 0.003792134 0.003754962 0.003708309 0.003651608 0.003584305 0.003505857 0.003415750 0.003313498 0.003198656 0.003070826 0.002929665 0.002774897 name: ``barnase_map.out`` .. code-block:: bash # Data from PBSAM Electrostat run # My runname is barnase_map.out and units kT grid 100 100 100 origin -25.025 -24.4258 -30.4642 delta 0.538326 0.493468 0.563884 4.8667332 -1.1809119 -8.3553659 0.2419499 5.1270905 -4.6114465 -7.2974789 0.2407265 5.5570112 -3.1729867 -7.2710317 0.2437944 5.7783599 -1.6880478 -7.2445845 0.2337809 5.9996470 -4.5953014 -6.0809087 0.2450571 name: ``barnase.y.0.dat`` .. code-block:: bash # Data from PBSAM Electrostat run # My runname is barnase.y.0.dat units kT/e grid 100 100 axis y -0.245894 origin -25.025 -30.4642 delta 0.538326 0.563884 maxmin 0.350066 -0.311879 0.0074041 0.0076604 0.0079257 0.0081997 0.0084821 .. _pbsam_dyn: 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 contact.barn_bars attypes 2 type 1 2 move 0.015 0.000045 pqr 1 barnase.pqr #pqr 1 barnase_cg.pqr # for after CG surf 1 barnase.vert xyz 1 1 pos_1_1.xyz xyz 1 2 pos_1_2.xyz type 2 2 move 0.015 0.000045 pqr 2 barstar.pqr #pqr 2 barstar_cg.pqr # for after CG surf 2 barstar.vert 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: ``barnase.pqr`` ( the first few lines) .. 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: ``barstar.pqr`` ( the first few lines) .. 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 name: ``contact.barn_bars`` .. code-block:: bash 1 872 2 1208 3.0 1 1565 2 538 3.2 1 894 2 541 2.8 1 862 2 566 2.9 1 425 2 671 3.0 1 1242 2 474 2.7 1 1249 2 631 2.5 1 1248 2 683 3.1 To run: .. code-block:: bash $$ ../../bin/pbsam 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