On 28/06/2011 8:09 PM, Anna Marabotti wrote:
Dear Tsjerk, dear all,
thank you very much for suggestion. One of the main reasons why I never used
the rhombic dodecahedron box for my simulations is the fact that it is
really hard to visualize the results with programs such as VMD or Pymol, and
therefore I cannot check easily during the setting of my system if the work
proceeds properly. Since I would like to redo my simulations following your
suggestion, could you please give me some hints on how to proceed in order
to visualize easily the system?
In my experience, "trjconv -pbc mol -ur compact" is the way to achieve this.
For example, now I created a dodecahedric
box filled with water and ions. I tried to visualize it with VMD and I saw
it as a rectangular box with the protein at one edge. I tried to use the
command trjconv:
trjconv -f prot_dod_box_neu.gro -s prot_dod_box_neu.tpr -o
prot_dod_box_neu2.gro -pbc mol -ur compact
and I obtained an error message stating:
Fatal error:
Index[84328] 84329 is larger than the number of atoms in the trajectory file
(84328)
The contents of the -f and -s files have to match meaningfully. Yours don't.
I'm surprised this error message is as cryptic as it is. I'll make it
less so.
I don't find this error neither in the gmx-users list archive (indeed it's
becoming harder and harder to search into this archive, given that each
message is visualized 10 times, as I already noticed sometimes ago), nor in
the Error section. The first .gro file is the one coming from genion, and
the .tpr file is the one I used to neutralize the system, which is the .tpr
file I should give to trjconv?
For "-pbc mol", trjconv needs to be told the definition of the molecules
in the -f file. So you need to supply a .tpr that corresponds to it.
Generating ions is a tricky case, because the output files do not match
the input .tpr. Hence its scarcity in the archives. However, since
you'll shortly be generating a .tpr file for the next stage, it's not a
real problem for visualization.
You see, if every time I try to use a box
different from the standard cubic one I has to deal with such maybe trivial
(for you) problems, but difficult and long to solve, I'm quite discouraged
to use it!
The only problem with the above is a small gap in understanding. I hope
I've filled that now.
This is also a kind request for Gromacs Web site managers: could
you please add a section for this (recurrent, I suspect) problem of box
visualization in the "How-to" section? it would be very useful for users, I
think, and probably also for you (less trivial questions posted to the
gmx-users list...)
The web page is a wiki - anyone with useful contributions is welcome to
make them, but registering an account for editing does require
registration. People who've experienced and solved a problem are often
well placed to document management strategies :-) Others will come along
and flesh out details, etc.
Mark
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