[gmx-users] problems when using trjconv or g_msd to process xtc trajectory files with only a portion of all the atoms in the system

Mark Abraham Mark.Abraham at anu.edu.au
Fri Aug 3 02:33:25 CEST 2012

On 3/08/2012 5:24 AM, rocwhite168 wrote:
> Thanks! Your suggestion 3 solves the problem!
> On Wed, Aug 1, 2012 at 2:25 PM, Christopher Neale
> <chris.neale at mail.utoronto.ca> wrote:
>> 1. does topol.tpr really correspond to traj.xtc? You don't need to specify -s to simply use the -b and -e options
>> to trjconv so simply eliminate that.
> Yes. topol.tpr matches traj.xtc. But indeed trjconv shouldn't need the
> structure file and removing -s topol.tpr option eliminates the
> problem.
>> 2. is there a file called index.ndx in that directory? That is the default name of the index file for trjconv input
>> and make_ndx output, so perhaps trjconv is picking up an index file that is not appropriate for this system.
> Usually no. Even in the case that there is such index file, index.ndx
> matches the system being analyzed.
>> 3. You say that only a portion of the atoms have been written to the .xtc. Do you mean that you did that straight
>> out of mdrun? Your trjconv should then work fine if you simply don't give it the .tpr file. To do analysis, you will
>> need to create a new .tpr file that has atoms corresponding to the ones that you wrote out. If, for example, you
>> did not write out the coordinates of one protein molecule, then make a new .top and .gro file corresponding to
>> that system and run them through grompp to get a new .tpr file. You can use this .tpr file for your analysis (but not
>> for simulations of the entire system).
> Yes. I set xtc-grps to contain only part of the system in grompp.mdp
> before generating the topol.tpr input file. Generating a new tpr file
> will indeed make the analysis tool happy. Thanks!!
> ---------------
> However, I think the analysis tools can be made a little more
> convenient, since generating a new tpr file means that all conf.gro,
> grompp.mdp, and topol.top have to be changed accordingly. This will be
> a lot of (meaningless) work -- or am I missing some easier approach
> again?
> ondering if I have missed anything.

tpbconv will make a subset of your .tpr directly (but do not attempt to 
run simulations with it). trjconv and/or editconf can deal with the 
other files similarly. You're just applying the same group selection to 
all the files.


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