Anna Duncan wrote:
Hi Justin,
Thanks for your speedy response. I've set off the simulation with the
checkpoint file rather than the trajectory and energy files and that
seems to be going fine now.
v4.5.3 g_energy showed the .edr file from the backbone-restrained run to
have no Xi-0-Protein term present, although the .edr file from the
equilibration run has a term called 'Xi-Protein'
It looks like there may be a bug in the code, related to the nhchainlength
parameter. The energy term names are now prefixed not by "Xi-" but "Xi-(chain
index)," for which the only value can be zero, as I understand the code in its
present form.
I'll look into this a bit more and file a bug report, if necessary.
-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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