VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Thu Jun 03 2004 - 07:22:09 CDT

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> 

-- 
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Dr. Axel Kohlmeyer                        e-mail: axel.kohlmeyer_at_rub.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/~axel.kohlmeyer/
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