pawan raghav wrote:
I have done 15ns MD simulations at 300k temp for a protein finally
obtained an average structure from g_rmsf. so please tell me is output
average structure is a sampled structure? is there no need of remd or
sampling further because I got plateau in RMSD calculation at last?
Some useful information:
http://www.gromacs.org/Documentation/Terminology/Average_Structure
I have strongly energy minimize by first steepest second by conjugate
gradient of my protein after simulation was completed. I have got 81%
residues in core region of RC plot by using this energy minimization
method. I have also used SPDBv instead of former one method for EM but
got 91% core region residues. Which methods should I choose to get the
good model? what are the essential criteria for a good model?
Energy minimization simply provides a reasonable starting structure for MD
simulation. Different methods can certainly produce different results; it's up
to you to determine what the functional significance of these changes might be.
-Justin
--
Pawan
--
========================================
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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