Re: Question about equilibration

From: snoze pa (snoze.pa_at_gmail.com)
Date: Wed Jun 15 2011 - 11:20:04 CDT

Please find the link to check the deformed protein

http://img10.imageshack.us/i/deform.png/

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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