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:
Physical Calculation run¶
Input Files¶
name: run.energyforce.inp
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
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
-10.0 23.4 -8.7
0.0 0.0 -2.5
To run:
$$ ../../bin/pbam run.energyforce.inp
Output Files¶
And the resulting file:
name: energyforce.2sp.jmol.out
My units are Joules/Mol
MOLECULE #1
POSITION: [-10, 23.4, -8.7]
ENERGY: 1328.86
FORCE: 1.19858e+08, [-36.6012 1.19858e+08 -1.65408e-05]
TORQUE: 1.78426e+06, [1.28425 1.78426e+06 1.9978e-06]
MOLECULE #2
POSITION: [0, 0, -2.5]
ENERGY: 1328.86
FORCE: 1.19858e+08, [36.6012 -1.19858e+08 1.65408e-05]
TORQUE: 1.78354e+06, [1.28372 1.78354e+06 1.99699e-06]
Electrostatics run¶
Input Files¶
name: run.electrostatic.inp
runtype electrostatics 140
runname electrostatic
units kT
salt 0.01
temp 298
idiel 4
sdiel 78
dx out.dx
3dmap electro_map.out
gridct 2
grid2D 1 out.x.0.dat x 0
grid2D 2 out.x.-1.dat x -1
attypes 2
type 1 2
pqr 1 single_charge.pqr
xyz 1 positions_2.xyz
type 2 2
pqr 2 pos_charge.pqr
xyz 2 positions_pos.xyz
The files for PQR and XYZ files are:
name: single_charge.pqr
ATOM 1 N NTR 0 0.000 1.000 0.000 4.0000 0.3200
ATOM 1 N NTR 0 0.000 0.000 -1.000 4.0000 0.3200
ATOM 1 X CEN 0 0.000 0.000 0.000 0.0000 2.0000
name: positions_2.xyz
0.0 0.0 -5.0
0.0 0.0 5.0
name: pos_charge.pqr
ATOM 1 N NTR 0 0.000 1.000 0.000 -4.0000 0.3200
ATOM 1 N NTR 0 0.000 0.000 -1.000 -4.0000 0.3200
ATOM 1 X CEN 0 0.000 0.000 0.000 0.0000 2.0000
name: positions_pos.xyz
0.0 5.0 0.0
0.0 -5.0 0.0
To run:
$$ ../../bin/pbam run.electrostatic.inp
Output Files¶
And the resulting files:
name: out.dx
# 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
# 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
# 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
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 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
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: 1BRS_chainD.pqr
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
To run:
$$ ../../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.
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