Halie Shah wrote:
Hi!
I have just completed a position restrained dynamics run on my protein
with GROMACS 3.3.3 and I generated an xvg file with the g_energy
command...I noticed in this that the energy for time step 0 was 0.88
(near 0) kj mol/S-1/N while the energy for time step 0.2ps was
1158....after this the rest of the time steps (up to 20ps) were roughly
around 1150. I'm wondering why the energy at the start is so low for my
protein (which I energy minimized)...I assumed it would be near 1150. Is
this a problem/what does it mean? Os it fine to move on and do an mdrun?
You'll have to be more specific about what's going on. Saying "energy" isn't
very informative. What were you looking at - potential, total, kinetic? Are
you generating velocities at the outset of the simulation?
-Justin
Thanks so much,
Halie Shah
University of Houston
Briggs Computational Biology Lab
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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