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:

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

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’).

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.

pqr 1 barnase_cg.pqr # _cg file has replaced pqr
#surf 1 barnase.vert # commented out, no longer needed

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.

pqr 1 barnase.pqr
imat 1 barnasesph

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.

pqr 1 barnase.pqr
exp 1 barnase

Physical Calculation run

Input Files

name: run.energyforce.inp

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)

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)

# 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

 0.0   0.0   0.0
12.0  12.0  12.0

To run:

$$ ../../bin/pbsam run.energyforce.inp

Output Files

And the resulting file:

name: gly_0.05M.out

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]

Electrostatics run

Input Files

name: run.electrostatic.inp

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)

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)

# 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

0.0   0.0   0.0

To run:

$$ ../../bin/pbsam run.electrostatic.inp

Output Files

And the resulting files:

name: barnase.dx

# 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

# 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

# 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

Dynamics run

Input Files

name: run.dynamics.inp

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)

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

61.25 61.25 61.25
-26.25 61.25 -26.25

name: barstar.pqr ( the first few lines)

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

-26.25 61.25 61.25
61.25 -26.25 61.25

name: contact.barn_bars

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:

$$ ../../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.

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.

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.

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