distance calculation between atoms of two segments

From: mjyang (mjyang_at_hku.hk)
Date: Sat Jan 22 2011 - 10:51:00 CST

Dear all,

  I performed a MD simulation for a protein+ligand+water system with periodic boundary conditions by NAMD. But when I calculated the distance between two atoms, one in ligand and the other in protein, some values of the distance is as large as 60 angstrom. After checking the dcd files, I noticed that in some frames, the ligand and protein were in different unit, e.g. protein in the primary unit and ligand in the neighboring image unit. Is anyone who encounters the same problem? Could someone please tell me how to fix it by distance calculation?

Many thanks.

Mingjun

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