[gmx-users] Switching from v4.0.7 to v 4.5.3 - being able to get the correct terms from a edr file when continuing a simulation

[Justin A. Lemkul]

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

========================================