[gmx-users] calc. average protein structure

Nuno R. L. Ferreira nunolf at ci.uc.pt
Thu Sep 16 13:05:09 CEST 2004

Hi Maarten

Perhaps with g_cluster.
If the protein doens't have large conformational changes during your simulation, I think you could do clustering of the run, and if I'm not mistaken, g_cluster has an option to spill out the average structure and/or the central structure of each found cluster.

Best regards,
  ----- Original Message ----- 
  From: Maarten Wolf 
  To: gmx-users at gromacs.org 
  Sent: Thursday, September 16, 2004 12:05 PM
  Subject: [gmx-users] calc. average protein structure


  Does anyone know how I can compute/calculate the average structure of my protein after an md simulation?

  Thanks in advance,

  Maarten Wolf

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