[gmx-users] Energy minimization result problem

[neha_bharty]

Hello Justin Lemkul

Thank you very much for your reply.
I also preformed MD for 15 ns. After MD I check my protein model with
Ramachandran Plot using Online Procheck server. But the result was same as
after energy minimization. The residues which were present in allowed region
was again less than that of previous protein.
As I am new in gromacs I don't have much idea.
In my view I guess after energy minimization and MD the residues which were
present in allowed region of Ramachandran plot should be increases.
And if it decreases it means the previous model is better.
Is there any other way to check my protein model is better after energy
minimization and MD or not??

If require I can also send the .mdb file I have used for MD.



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