Dear Berk,
Thanks for the quick reply. That leads me to my next questions:
*I used the whole N and C residues for pulling. Is there any way of
reconstructing the values for the single atoms? Or do you recommend
only to pull N and C in the first place?
*What does the reference group actually do? Can I simply leave it out?
Does it influence pulling? What would be a good reference group? A
random backbone atom from the middle of the protein?
I'm looking forward to your reply. Thank you very much in advance.
Best wishes, Ilona
Quoting Berk Hess <[email protected]>:
Hi,
This is actually not (yet) documented.
0Z is the Z-coordinate of group 0.
1dZ is the the Z-coordinate of group 1 minus the one of group 0.
Berk
Date: Tue, 23 Jun 2009 12:54:37 +0200
From: [email protected]
To: [email protected]
Subject: [gmx-users] pullx.xvg Meaning of output?
Hi!
I am trying to understand the output of my pulling simulation:
I get a pullx.xvg file which shows 0Z, 1dZ, 2dZ after pulling in Z and
-Z direction. I really cannot figure out the meaning of 1dZ and 2dZ.
Since the website is down I cannot check on previous issues, so sorry
for asking the same question again as I already asked last week but
which remained unanswered.
I would appreciate any advice.
Thanks a lot. Ilona
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Ilona Baldus
MPI Stuttgart
INF 276
69120 Heidelberg
Tel.: 06221-5451268
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