[gmx-users] g_covar

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Jun 1 21:05:33 CEST 2010


Fitting is commonly done mass weighted if the reference file contains
masses, like a run input file. But covariance analysis is only
performed mass weighted if explicitly requested (and masses are
available). If mass-weighted analysis is not requested, the masses for
the fit will all be set to one, so as to assure that the fit and the
analysis will concern the same thing. That is what the message is
trying to tell. So no problem (unless you wanted mass-weighted

Hope it helps,


On Tue, Jun 1, 2010 at 8:51 PM, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> ----- Original Message -----
> From: pawan raghav <pwnrghv at gmail.com>
> Date: Wednesday, June 2, 2010 4:18
> Subject: [gmx-users] g_covar
> To: gmx-users at gromacs.org
>> Thanks Mark for your advice
>> Note: The fit analysis group are identical, while the fit is mass weighted
>> and the analysis is not making the fit non mass weighted.
>> But, this is the the real unning out put of the command prompt
> No, it isn't. :-) I've now consulted the 4.0.7 source code, this message
> would have had a full stop and a capital M. Since they were missing, it
> looked like you were saying something confused.
> g_covar won't do a mass-weighted fit with a non-mass-weighted analysis.
> g_covar -h talks about this.
>> 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?   >
>> Yes I want to do the structure-fitting on the same set of atoms as I do
>> the analysis.
> Well, then you need to make a choice consistent with that.
> Mark
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands

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