[gmx-users] homodimer simulation

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 10 15:59:13 CET 2012

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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