Re: AW:

From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Wed Nov 26 2014 - 09:53:23 CST

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Hi Norman,
You give me the clue I needed.
Problem solved.

Thank you.

Flavio

________________________________
 From: Norman Geist <norman.geist_at_uni-greifswald.de>
To: namd-l_at_ks.uiuc.edu; 'flavio seixas' <oivalf_nix_at_yahoo.com>
Sent: Wednesday, November 26, 2014 6:26 AM
Subject: AW:
 

Did you wrap in VMD or
in NAMD ?
 
Norman Geist.
 

Von:owner-namd-l_at_ks.uiuc.edu
[mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von flavio seixas
Gesendet: Mittwoch, 26. November 2014 02:13
An: Namd Mailing List
Betreff:
 
Hi,
During a simulation, the protein crossed the periodic box.
When analyzing the RMSD, I realized that this fact interfered in the
calculation because rmsd was stable until half simulation. When protein cross
the periodic border, the rmsd value abruptly increase 10 times.
I searched for similar questions in namd-list but nothing was found.
Any suggestions on how to compensate this fact?

grateful for any help

Flavio
 

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