RMSD of backbone changes rapidly at the beginning of production run

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Thu Nov 02 2017 - 04:52:11 CDT

Dear all,

I did a MD simulation of an amino acid chain in water having strong
constrains applied to backbone atoms. Prior to the production run I
equillibriated the system in constant temperature and pressure and used the
extended system files to start the production run. When I calculated the
RMSD of the backbone, I expected to see a minimal fluctuation in RMSD but I
see a sudden increase in RMSD just after the simulation is started and then
it follows a damped oscillatory behavior before it reaches an asymptotic
value. I wonder what could be the reason for that kind of a behaviour, is
it due to something wrong with my configuration parameters?

Thank you.
Best regards,

W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.

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