Re: Question about equilibration

From: johan strumpfer (johan.ks.uiuc_at_gmail.com)
Date: Wed Jun 15 2011 - 11:19:17 CDT

It is unclear what you mean by "deformed" but some structural change
is usually expected. A total equilibration of 1 ns is usually not very
much and I would run longer. You should check to see if the rmsd has
plateaued to get an indication of whether you have equilibrated the
system.

Cheers,
Johan

----------------------------------------------------------------
Johan Strumpfer (johanstr_at_ks.uiuc.edu)
Theoretical and Computational Biophysics Group
3115 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801, USA

On Wed, Jun 15, 2011 at 11:07 AM, snoze pa <snoze.pa_at_gmail.com> wrote:
> Dear NAMD Users,
>
>
> I need some explanation regarding my protein equilibration. I see my protein
> gets deformed during the equilibration. Do you think it is okey?
>
> To add one more note about the protein deformation. First I used harmonic
> constrained during the equilibration. Then the restrain were removed and
> protein was again equilibrated. I am getting deformation after removing
> harmonic constraints. In this step during first 600 ps it is fine but last
> 300 ps the protein is getting deformed.
>
> I will highly appreciate your help.
>
> Thank you
>
> S
>
>
>

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