[gmx-users] Visualizing of a peptide in a water box - usingtrjconv

[Kukol, Andreas]

For presentations it may be the best to show first the diffusion of the protein in the box and then say that you now focus on the protein internal motions in the next slide.


> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Birgit Hischenhuber
> Sent: 01 June 2010 15:57
> To: 'Discussion list for GROMACS users'
> Subject: AW: [gmx-users] Visualizing of a peptide in a water box -
> usingtrjconv
>
> Aha, ok. Thank you!
> And do you consider that the first or the second visualizing is better for
> presentations?
>
> Regards, Birgit
>
> -----Ursprüngliche Nachricht-----
> Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] Im
> Auftrag von Kukol, Andreas
> Gesendet: Dienstag, 1. Juni 2010 16:49
> An: Discussion list for GROMACS users
> Betreff: RE: [gmx-users] Visualizing of a peptide in a water box -
> usingtrjconv
>
> I don't think there is that possiblity, because protein diffusion is a
> natural process that occurs in your simulation.
>
> Andreas
>
> -----------------------
>
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Birgit Hischenhuber
> Sent: 01 June 2010 15:24
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Visualizing of a peptide in a water box - using trjconv
>
> 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
>
> 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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