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

[Berk Hess]

Hi,

Everything depends on what you want to accomplish, which you
do not write.
I don't see why you would want to look at single atoms.
Since you pull on COM's, only the COM coordinates are relevant.
If you want to look at single atoms, simply store them in the xtc file.

If you have only two groups, there is no physical difference between
the reference group and  the first pull group. They are simply two
groups between which the distance is calculated and the forces act.
If you used an absolute reference, 0Z is the absolute reference coordinate,
not the coordinate of a group.

Berk

> Date: Tue, 23 Jun 2009 14:39:48 +0200
> From: ilona.baldus at bioquant.uni-heidelberg.de
> To: gmx-users at gromacs.org
> Subject: RE: [gmx-users] pullx.xvg  Meaning of output?
> 
> 
> 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
> >> _______________________________________________
> >> gmx-users mailing list    gmx-users at gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at http://www.gromacs.org/search before posting!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-request at gromacs.org.
> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> > _________________________________________________________________
> > Express yourself instantly with MSN Messenger! Download today it's FREE!
> > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
> 
> 
> 
> Ilona Baldus
> MPI Stuttgart
> INF 276
> 69120 Heidelberg
> Tel.: 06221-5451268
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_________________________________________________________________
See all the ways you can stay connected to friends and family
http://www.microsoft.com/windows/windowslive/default.aspx
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090623/3c7aa96b/attachment.html>