Andrew DeYoung wrote:
Justin,
Thanks. So I imagine that the order that the atoms are "stepped through" is
dictated by the order of atoms in the configuration file (.gro or .pdb); do
you think that this is correct? I am not simulating a protein, so other
than the order of atoms in the configuration file, for my system there is
not any obvious order to use (such as N terminus, H attached to N terminus,
C-alpha, etc).
Yes, from everything I can tell the order that is used is the one found in the
coordinate file.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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