shahid nayeem wrote:
Thanks Justin
I have pulled one of the chain from an initial COM distance value of
3.65 A to 7.90 A. When I look this trajectory in VMD I find that the
I will have to assume you mean nm. Gromacs does not deal in Angstrom, and these
distances would be within any sensible short-range cutoff and thus not
indicative of actual separation.
chain is completely separated. But even at this separation the
profile.xvg file does not show its convergence to one value. I sent this
file to you earlier.
Sorry, I don't have a photographic memory, nor can I recall if you've ever
posted your .mdp file, or at the very least, told us how much sampling you've
done in each window. It may well be that your simulations are simply too short
to observe adequate post-equilibration sampling.
-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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