how to calculate the box size

From: mjyang (
Date: Tue Mar 06 2012 - 01:48:45 CST

Dear NAMD users,

     I performed a simulation by NAMD for a protein system solvated by a cubic water box. Now I extracted the snapshots from NAMD trajectory for postpone analysis, in which the protein should be centered in the box. The box size was calculated by (max_x-min_x, max_y-min_y, max_z-min_z), where max_x,y,z and min_x, y, z are the maximum and minimum coordinate values of the extracted frame. However, the box size calculated in this way is a little larger than the real one, resulting in gaps in the recentered box. It seems that the box size written out by NAMD in the *.xsc file is better than what I calculated. But the NAMD output size (in *.xsc file) only corresponds to the last frame of a segment of trajectory file and I need the size for each frame in the traj. Could someone please tell me how NAMD calculate the box along MD simulations?

Many thanks.


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