Data Formats

2. Data Formats

2.1 Input Data Format

The software has two input data files, the coordinates input file (init_positions_small for the system with 6860 atoms and init_positions_big for the system with 54880 atoms) and the data input file (md_small.dat for the system with 6860 atoms and md_big.dat for the system with 54880 atoms). The format for the data input file should be as follows:

6860 NTOT

number of particles

1.0000 EPS

epsilon (kJ/mol)

0.3000 SIGMA

sigma (nm)

20.0 WMASS

mass (amu)

8.09202 BOX

box length (nm)

50 NSTEP

number of dynamics steps

0.0100 DT

time step (ps)

300.0 TBATH

initial temperature (K)

17841 IG

random number seed

1.00 RCUT

LJ cutoff distance (nm)

10 NTPR

print energies every NTPR steps

1000 NTWX

write coordinates every NTWX steps

1000 NTWE

write energies every NTWE steps

Basically the constraint is that the values should occupy at most the first 10 characters of each line and the order of the property – value pairs should be preserved i.e. NTOT should always be the first line, followed by EPS etc.

The format of the coordinates input file should follow the pdb (protein data bank) format. For more information on the pdb format, please refer http://www.umass.edu/microbio/rasmol/pdb.htm. The first few lines of the coordinates input files are as follows:

ATOM 1 B B 1 -20.512 7.215 33.289 0.00 0.00 ATOM 2 B B 2 -22.849 1.471 -25.234 0.00 0.00 ATOM 3 B B 3 40.181 -34.958 10.244 0.00 0.00 ATOM 4 B B 4 27.884 19.728 -18.005 0.00 0.00 ATOM 5 B B 5 -18.798 15.000 5.051 0.00 0.00 ATOM 6 B B 6 -1.832 10.136 39.148 0.00 0.00 ATOM 7 B B 7 -29.855 18.356 22.965 0.00 0.00

For the purpose of this project, the constraints are 1) the total number of lines in this file should be equal to the number of atoms in the simulation system and 2) the x, y and z For the purpose of this project, the constraints are 1) the total number of lines in this file should be equal to the number of atoms in the simulation system and 2) the x, y and z

For testing purposes, the velocities have to be read from the file “vel.in” (this is only for the system with 6860 particles). The total number of lines in this file should be equal to the number of atoms in the simulation system and the format is shown as below (the first few lines in the file are shown):

-0.468415343794807 0.366741958309217 0.798061712445195 2.630747657094827E-002 -6.747689914408322E-002 -7.582933435198365E-002 -0.617412010567999 0.339550740206594 -0.167975555032691 0.585295550026653 -0.191146826899770 0.293272860486950 6.131226309386512E-002 -0.182546512969571 -0.365545674040731 0.106814174639356 -0.107245268069441 -0.423193642978872

Basically, the constraint is that the each of the velocities in a line should be within the allocated number of characters for it which is 24, i.e. the x coordinate of velocity should

be within the first 24 characters, and the y coordinate of velocity should be within the next 24 characters and so on.

2.2 Output Data Format

There are two output files for this program: final_positions: The final coordinates in all directions (x, y and z) of each atom are written to this file after the end of the simulation. The format of the file is similar to the coordinates input file.

md.out: The energies and the temperature at every given number of time steps are written to this file. Also written at the end of the file are the averages and fluctuations of md.out: The energies and the temperature at every given number of time steps are written to this file. Also written at the end of the file are the averages and fluctuations of

Time Step Time (ps) TE PE KE TEMP