Kavyashree M wrote:
Dear user,
I simulated a homodimer of 238aa each with oplsaa forcefield
using gromacs-4.5.3. But while calculating the rmsf plot I got a
plot in which starting and ending residue were connected by a
straight line along with the actual rmsf plot. Also the two rmsf
That's probably some artifact of the plotting software and is not actually
relevant.
plots that it gave were slightly different from each other in few
regions. I was expecting similar rmsf for both the monomers.
If they are "slightly different," that does not necessarily mean they are
"significantly different," and what you are observing is likely nothing more
than the stochastic nature of MD. Did you run only one simulation, or multiple?
How did you assess convergence? It is highly unlikely to me that any MD
simulation will produce identical results, but rather will be within some
definable value of standard deviation, standard error, etc.
I checked the pdb file generated after md run, it did not have chain
ID but two chains were present.
Kindly let me know what is wrong with rmsf? Or what is wrong with
simulation.
Likely nothing.
-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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