[gmx-users] g_covar Segmentation fault

Nicolas nsapay at ucalgary.ca
Wed Apr 15 15:02:55 CEST 2009

Anirban Ghosh a écrit :
> Hi ALL,
> I have a system of beads with which I ran a CGMD (coarse grained MD) 
> using NAMD. Now I want to do a PCA analysis of this system using 
> GROMACS. So I converted the trajectory in .trr format
Convert a dcd file into a trr file is not that straightforward. How did 
you do that?
> and made an index file of the entire system (45 beads). But now when I 
> try to run g_covar using the group consisting the entire system, for 
> least square fit and covariance analysis, it is giving Segmentation 
> Fault. Am I doing anything wrong. Any suggestion is welcome.
You probably also need a tpr file. To create it, you need the parameters 
of your force field (in Gromacs format), the topology of each molecule 
you've got in your system (still in Gromacs format) and to run grompp.  
Depending on the original format of your force field, in can be quite 
difficult to do the file format conversion.

Hope that helps...
> Regards,
> *Anirban Ghosh*
> *Grade Based Engineer
> Bioinformatics Team
> Centre for Development of Advanced Computing (C-DAC)
> Pune, India
> *
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