[gmx-users] add timestamp to frames

[David]

On Tue, 2003-07-15 at 17:29, barrett wrote:
> Hi
> 
>  
> 
> Summary: 
> 
> how do you add timestamps to a set of pdbs in a trajectory saved from
> VMD.
> 
>  
> 
> Background:
> 
> I have a concatenated set of pdb files without any time stamps on the
> frames.
> 
> I want to process them with g_covar. However g_covar dies immediately
> complaining about too many iterations in jacobi.
> 
> I think this is because it is trying to read the timeframe and cannot
> find it.
> 
>  
> 
> THEREFORE: I want to add timestamps to the frames of the trajectory.
> 
>  
> 
> I tried taking the individual frames as PDB files and then:
> 
>  
> 
> trjconv -f X.pdb -o X.xtc -t0 1
> 
> trjconv -f Y.pdb -o Y.xtc -t0 2
> 
> etc..
> 
>  
> 
> followed by 
> 
>  
> 
> trjcat -o ensemble.xtc *aligned.xtc

This works for me (using CVS code) 

An alternative is to trjcat the pdb files directly if necessary with the
-settime option 

remember the -h flag is your friend... (I don't know all those options
either)
> 
>  
> 
> but this failed:
> 
>  
> 
> Last frame         0 time    1.000
> 
> Fatal error:
> 
> Couldn't read time from second frame.
> 
>  
> 
> Suggestions very much appreciated
> 
>  
> 
> Paul
> 
>  
> 
> Dr Paul Barrett
> 
> Laboratory of Molecular Biophysics
> 
> Department of Biochemistry
> 
> University of Oxford
> 
> Oxford
> 
> OX1 3QU
> 
>  
> 
> Tel 01865 275191
> 
> Fax 01865 275182
> 
>  
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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