[AMBER] PBC in umbrella sampling

From: dhacademic <dhacademic.gmail.com>
Date: Fri, 18 Jun 2010 10:45:14 -0400

I have a question about PBC in umbrella sampling.

The distance between active site and ligand is defined as the reaction coordinate. PBC with truncated octahedron as well as iwrap=1 are used. During the simulations of some windows in Umbrella sampling, the protein and its ligand will drift over time out of the primary unit cell. It looks to stay on one side of the cell box while the ligand appears on the other side of the box. In principle, this should be OK as the implement of PBC.

However, the calculated coordinate is much longer than the restraint one (as shown on the output attached below). It seems that the calculated coordinate is the distance between protein and one image structure of ligand. What is wrong? Thanks in advance.

  138000 7.070
  138500 7.172
  139000 61.263
  139500 7.239
  140000 7.118
  140500 7.126


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Received on Fri Jun 18 2010 - 08:00:04 PDT
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