VMD-L Mailing List
From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Thu Jun 03 2004 - 12:44:37 CDT
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- In reply to: Ran Friedman: "Re: CUBIC box of system"
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On Thu, 03 Jun 2004 15:56:23 -0400 Ran Friedman wrote:
> Hi,
>
> Will it work also for non-cubic boxes?
not as it is. there is a version for orthorhombic
unitcells in my vmd download area, though.
i have always planned to do a generic version,
that does read the unitcell information from VMD
directly (if it is read in with the coordinates),
but so far there was always something more urgent
to do... <g>
axel.
>
> Ran.
>
> Axel Kohlmeyer wrote:
>
> >On Thu, 3 Jun 2004, Raghunadha Reddy Burri wrote:
> >
> >RB> Dear all,
> >RB>
> >RB> How can I possible to see CUBIC box of system in VMD, this system from gromacs
> >RB> 3.2 output file (.gro).
> >
> >please have a look at
> >http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part2.html#chap4_sect6
> >
> >note, that gromacs uses nanometers, but the script expects angstroms.
> >
> >RB>
> >RB> And also I have interest to see H-bonds between two proteins in that system.
> >RB> Please help me in VMD.
> >
> >just add a hydrogen bonds representation to your system
> >and change the selection to 'protein'. have a look into
> >the VMD manual for a more detailed description of how to
> >do this.
> >
> >hope this helps,
> > axel kohlmeyer.
> >
> >RB>
> >RB> Thank you very much for your time
> >RB>
> >RB> Till Then
> >RB>
> >RB> Burri
> >RB>
> >RB>
> >
> >
> >
>
-- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de ======================================================================= If you make something idiot-proof, the universe creates a better idiot.
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