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
<[email protected]> 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.
Mark
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