Coordinates

Although the topology, the force field parameters and the input options have been discussed until now, one of the most important input files is of course the file containing all the coordinates of the particles in the system. As with the topology files, such a file exists for every molecule type. For example, a bilayer/water systems consists of two types of molecules (lipids and water) and hence there is a coordinate file for both the lipid and the water.

To be able to start a simulation at least as many coordinate files as molecules for the initial time step need to be present. Assuming that the simulation starts at time step 0, the name of an initial coordinate file for a DPPC molecule looks like DPPCIT0.pcf. This file can be either in binary or in text format. PumMa checks the file format and uses the same format for the output of coordinate files.

Depending on the input parameter Crep, which gives the frequency at which the system needs to be dumped to file, many more coordinate files may be created during the simulation. Similar to the configuration file the numbers following the sequence IT change according to the iteration at which the dumping occurred. For instance when both the bilayer (DPPC) and water (W) coordinates of a simulation were to be dumped at iteration 1250, both files are named DPPCIT1250.pcf and WIT1250.pcf.

The number of lines in a coordinate file depends on the number of molecules of that specific type and the number of particles within each molecule. Hence, the total number of lines is the multiplication of the number of molecules specified in the configuration file and the number of particles in that molecule as found in the corresponding topology file. For instance with 128 lipid molecules, each consisting of 12 particles, the total number of lines in the coordinate file for the lipids equals 1536.

The coordinate file is sorted by molecule, which means that first all coordinates of one molecule of that type are given, and thereafter of the second molecule of that type, and so on.
CAUTION The order at which coordinates for one molecule are stored in the coordinate file is given by the order at which they are specified in the topology file.

Besides the three cartesian coordinates of each particle, the corresponding velocities of that particle are also in the coordinate file. Consequently, a coordinate file has six columns, the first three for the positions and the last three for the velocities. A text-based extract of a coordinate file might look like

   ...
   1.7403    1.7556   20.3906    0.0501   -0.3916    0.1825
   7.5506   23.5415   12.4250   -0.3183    0.6467   -0.4984
  12.3325   11.7496   10.4196    0.5211   -0.2126   -0.0272
  26.1005   25.6564   12.1360   -0.0743   -0.1620   -0.5478
  ...

Of course to ensure correct behavior of the simulation the total linear momentum should equal zero, and hence, the velocity components each have to be distributed normally with zero mean. At startup and at regular intervals (specified by the lmrep input option) the linear momentum is set to zero by scaling all the velocities.

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