----- Original Message -----
From: Birgit Hischenhuber <birgit.hischenhu...@meduniwien.ac.at>
Date: Wednesday, June 2, 2010 0:44
Subject: [gmx-users] Visualizing of a peptide in a water box - using trjconv
To: gmx-users@gromacs.org
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> Hi,
>
> I simulate a peptide in a water box with some ions to get a neutral
solution. I want to visualize the peptide in the water box.
> I want that the peptide is in the center of the box, but also have a look
at the water.
>
> Therefore I tried two things:
>
> trjconv –f a.trr –o b.xtc –s c.tpr –skip 10 –pbc mol –ur compact –center
–fit progressive
>
> Visualizing it with VMD I see the peptide centering in the middle of the
box, but the water get during the time holes.
>
> So I checked the mailing list and find some inputs and tried it with two
steps:
>
> trjconv –f a.trr –o b.xtc –s c.tpr –pbc mol –ur compact
> trjconv –f b.xtc –o d.xtc –s c.tpr –skip 10 –center –fit progressive
I don't think -ur or -fit are useful for your problem. I suspect something like
trjconv -center
trjconv -pbc mol
is what you want, perhaps even in one pass. Obviously, check trjconv -h for
info - it suggests the combination of the above...
Mark
> at this try I get a peptide in the center of the box and during the time
the pepide moves to the edge of the box and I consider that the box rotate
around the peptide.
>
> Is there a possibility that my peptide stays in the center of the box and
the water doesn’t get any holes?
>
> Thanks a lot for your helps!
>
> ---
>
> DI Birgit Hischenhuber
> Unit for Medical Statistics and Informatics
> Section for Biomedical Computersimulation and Bioinformatics
>
|
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