[gmx-users] Position restrained..

[pawan raghav]

Dear All,

Hope this mail will find you in good health.

I am facing a problem regarding Position restrained dynamics (PR). I have
done Molecular dynamic simulation
(for cytosolic protein) but has not performed PR. So i m little confused if
this effects the results and if yes to what extent it effects the outcome,

Earlier, i performed PR as it is recomended but in my cases ,the generated
structure was not correct as the core residues found to be
reduced from 82%-52% and one bad contact was also observed. So i skipped the
PR Step and run MD
simultaion just after energy Minimization.

I was wondering if PR is always necessary before molecular simulation
without any exception. And if not, how can i justify this protocol
that we have performed without PR. Or where i can find the references to
justify the my protocol.

Pawan Kumar Raghav
Bioinformatician
Stem Cell and Gene Therapy Research Group
Division of Radiation Biosciences
INMAS, DRDO
Timarpur Delhi-110054

-- 
Pawan Kumar Raghav
Bioinformatician
Stem Cell and Gene Therapy Research Group
Division of Radiation Biosciences
INMAS, DRDO
Timarpur Delhi-110054
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