Re: Question about equilibration

From: snoze pa (snoze.pa_at_gmail.com)
Date: Wed Jun 15 2011 - 11:07:51 CDT

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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