[gmx-users] Vizualization with VMD: no image appears

[tarak karmakar]

vmd protein.trr protein.gro

then go to the representation and then write 'all not water' with
cartoon representation, u will get the protein only.

Cheers,
Tarak

On Thu, Nov 22, 2012 at 12:58 PM, rama david <ramadavidgroup at gmail.com> wrote:
> Dear,
>    -o MT.PnoH.xtc instad of xtc extenstion use pdb you will get pdb file.
> And then load it in vmd or pymol u can see it
>
> On Wed, Nov 21, 2012 at 10:24 PM, Rausch, Felix <frausch at ipb-halle.de>wrote:
>
>> Hi.
>>
>> Try to load in a .gro file of your system first. After that, use the "load
>> data into molecule" option to load in the .xtc.
>>
>> -----Ursprüngliche Nachricht-----
>> Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
>> Im Auftrag von shch406
>> Gesendet: Mittwoch, 21. November 2012 17:47
>> An: gmx-users at gromacs.org
>> Betreff: [gmx-users] Vizualization with VMD: no image appears
>>
>> Dear Gromacs users
>>
>> To visualize my trajectory with VMD I applied trjconv to .xtc trajectory
>> file to eliminate water molecules and velocities remaining protein
>> coordinates only.
>> However, when I load this reduced file to VMD no image on screen appears,
>> nevertheless VMD have identified the file as a "Gromacs compress trajectory
>> file".
>> What may be the cause of this?
>>
>> The corresponding command is as follows:
>>
>> trjconv -f MT.xtc -o MT.PnoH.xtc skip 1 -n defau.ndx -pbc nojump -novel
>>
>> where MT.xtc contains ~10 frames, defau.ndx is default groups index file.
>> Group 2 (Protein-H) was chosen handling dialog.
>>
>> Merci pour votre collaboration,
>> Igor Shchechkin
>>
>>
>>
>>
>> --
>> View this message in context:
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>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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