.xmol

This is plain text trajectory format, which can be produced by many molecular modeling packages, including MagiC. It consists of a number of consequent frames, with each frame having the following structure:

line 1:

Number of atoms in the frame (N)

line 2:

A commentary line

line 3:

Name(atom1) X(atom1) Y(atom1) Z(atom1)

line 4:

Name(atom2) X(atom2) Y(atom2) Z(atom2)

lines 5,6...,N+2:

Names and coordinates of atoms 3 - N.

In case of trajectory, configuration files from each time frame are written consequently one after another.

There is no common requirements for the commentary (second) line. For CGtraj module of MagiC it is assumed that the second line of each configuration follows this format (accepted in MDynaMix):

(char) <time> (char-s) BOX: <box_x> <box_y> <box_z>
where (char) is any character word, <time> is time in $fs$, <box_x> <box_y> <box_z> (following after keyword BOX). The length unit is Ångströms and time unit is femtoseconds. The time step information is not needed for CGTraj but the box size information is essential. If no box size information is present in the trajectory, the box size information can be supplied in the input file, but the later has a sense only in constant-volume simulations.

In xmol-files produced by MagiC the second line may have no time-stamp and box sizes.