[gmx-users] g_mdmat truncation distance for contacts

rajat desikan rajatdesikan at gmail.com
Tue May 13 08:07:22 CEST 2014

Hi All,
g_mdmat computes uses the truncation distance for residue contacts by
considering the minimum distance between residues. However, the papers I
referred to has a Calpha-Calpha or Cbeta-Cbeta cutoff of 10-12 angstrom
(default g_mdmat truncation criteria is 1.5 nm). Can anybody give heuristic
suggestions about the truncation distance value?

Thank you all for your time.


Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore

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