[gmx-users] Averege structure

pawan raghav pwnrghv at gmail.com
Wed Jul 21 07:46:48 CEST 2010

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?

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?

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