you can conclude that your system is in a local
minimum. It suggests (but does not prove) that
transitions out of that minimum take >1ns,
and it says nothing about the relative free energy
of this minimum relative to any other that was
never sampled.
In summary, it doesn't really tell you too much
other than there were no very bad contacts in the
initial structure. Whether this is sufficient depends
on the questions the simulation is supposed to address.
Carlos
----- Original Message -----
From: "Do Anh Tuan" <datuan.hcmuns.edu.vn>
To: <amber.scripps.edu>
Sent: Monday, October 20, 2003 1:30 PM
Subject: AMBER: stable protein
> Hello,
> I have 1ns MD simualtion with protein in water box. The change of RMS is
> not significant in comparison with the start. May I conclude the stable
> protein from this result?
> I am a new user.
> Thank you so much in advance.
>
> Tuan
>
> -----
> CBL UNS-HCMC, Vietnam
>
>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Mon Oct 20 2003 - 18:53:01 PDT
