[gmx-users] C-alpha group

Mark Abraham mark.abraham at anu.edu.au
Tue Jun 1 10:03:30 CEST 2010

----- Original Message -----
From: pawan raghav <pwnrghv at gmail.com>
Date: Tuesday, June 1, 2010 17:56
Subject: [gmx-users] C-alpha group
To: gmx-users at gromacs.org

> Hi friends, 
>                 For ED sampling I have used mdrun command to simulate about 59 residue protein (hypothetical model) then used g_covar to get eigenvec.trr and eigenval.xvg files. But while using this command it asked to chose a group two times, so according to this I have choosed C-alpha group for two time. But it showed a note i.e. the fit analysis group are identical, while the fit is mass weighted and the analysis is not making the fit non mass weighted.

As always, people will be much more intesreted in seeing a copy of your command line and a copy of the actual output, rather than something that's been filtered through your head. For example I think you mean "i.e. the fit AND analysis group are identical". You've made it hard for people to be sure they're spending their valuable time by actually helping you on the relevant issue, which means they might not bother at all...

> Please let me know anyone what is the meaning of this note? and also tell me is it right to choose C-alpha group for two times?   > 

That's your decision. Do you want to do the structure-fitting on the same set of atoms as you do the analysis?


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