[gmx-users] extract conformations !!

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jun 9 18:09:54 CEST 2008

Anamika Awasthi wrote:
> Dear Friends,
>        I want to extract conformations of each 1 ns from my 10 ns 
> simulation.
>        My this job is running for 20 ns, so shall I first stop my job 
> and then do this?

That won't be necessary, but there's no particular guarantee that all of 
your files are in sync, because of the system's I/O buffering.

>        I tried this command without stopping my job
>         trjconv -f *.trr -o *.pdb -s *.tpr -b -0 -e -10 -dump -1000
>        Please tell me the solution of my this problem

http://wiki.gromacs.org/index.php/Doing_Restarts  and 
http://wiki.gromacs.org/index.php/Using_Trajectory_Information have 
information useful to you, however your answers really are there in the 
man page of trjconv. However, unless you happen to have exactly one 
.trr, .pdb and .tpr file in your working directory, your shell globs 
will not work. Only a handful of tools in GROMACS permit such multiple 
I/O and trjconv is not one of them. You can tell by the suffix "Input, 
Mult." on the man page... viz

        -f traj.xtc Input, Mult.
         Generic trajectory: xtc trr trj gro g96 pdb"

Next, as the header of each man page indicates, only the flags that 
label the inputs get hyphens, not both the flags and their input data. 
This allows the code to distinguish flags from inputs to flags.


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