Re: RMSD of backbone changes rapidly at the beginning of production run

From: Peter Freddolino (
Date: Thu Nov 02 2017 - 09:02:13 CDT

You would need to provide more information, such as your config files and
how you measured the rmsd, in order to get a useful response...

On Thu, Nov 2, 2017 at 5:52 AM, Monika Madhavi <>

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

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:40 CST