radius of gyration

From: Peter Gannett <pgannett_at_hsc.wvu.edu>
Date: Mon 11 Sep 2000 13:24:10 -0400

Amber users:

We are trying to determine the rotation about a bond in the group R(R)N-O with respect to time. Carnal has a group operation called radius of gyration which seems like it should be useful for this purpose. But I'm not exactly sure what this command dumps (the carnal input file is below, residue 8 is a modified base that contains the R(R)NO group along with 49 other atoms and the output varies about 3-4).

What are the units of this number, Angstroms, and what is the reference point - is the center of mass used or a geometric center or something else. Finally, is there a way to apply the radius of gyration to only the atoms of interest.

Perhaps the real question is can carnal/radius of gyration be used to determine the angular rotation of the group of interest and if not, what analysis tools could be used for this purpose regardless of whether they are a part of Amber or not.

  PARM p1 tat5m_md_nowatNA.top;
  STREAM s1 tat5m_md_prod_nowatNA.traj;
  TABLE t1 radgyr.tbl;
  GROUP grpid1 (RES 8);
  TABLE t1 grpid1%radgyr;

Pete Gannett
Received on Mon Sep 11 2000 - 10:24:10 PDT
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