[gmx-users] help - projection values

Lakshmi Padmavathi lpulagam at uos.de
Mon Oct 16 18:00:00 CEST 2006

Dear gromacs users,

I am very new for using essential dynamics. I request your help to
understand some of my results.

1. In essential dynamics analysis, the average of projection values (for
eigenvector 1) is not nearer to zero. The min and max projection values
along trajectory are
Min = -1.6
Max = -4

What does it mean? This happens to me when I projected the trajectory along
eigenvector 1 only. For other eigenvectors it is fine.

2. In my analysis of different simulations, the projections along
eigenvector 1 are either completely positive or negative. They are not like
amadei et.al(1993) in which they are crossing zero.

Is there anything wrong in my simulations?

(I did simulations for 10ns)

Could any of you help me? i will be very thankful to you for your help.

Best regards, 

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