[gmx-users] pullx.xvg Meaning of output?

[ilona.baldus at bioquant.uni-heidelberg.de]

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 <gmx3 at hotmail.com>:

>
> 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: ilona.baldus at bioquant.uni-heidelberg.de
>> To: gmx-users at gromacs.org
>> 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