[gmx-users] Visualizing the simulation in VMD

[bharat gupta]

On Thu, Jan 20, 2011 at 7:44 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> bharat gupta wrote:
>
>> I loaded the .gro file generated after pdb2gmx command in vmd and then I
>> loaded the .trr file into that molecule but it shows frame 1 vol 0 in VMD
>> and when I click the play button on the toolbar the frames doesn't move ...
>> can anybody tell me how to play the simula tion in VMD ?? or where am i
>> going wrong
>>
>>
>>
> How many frames did you save in the .trr file?  Use gmxcheck.  If it has
> multiple frames, it will load them all and you can watch the movie.  Sounds
> like you haven't saved enough frames.
>
> -Justin
>
>  --
>> Bharat
>> Ph.D. Candidate
>> Room No. : 7202A, 2nd Floor
>> Biomolecular Engineering Laboratory
>> Division of Chemical Engineering and Polymer Science
>> Pusan National University
>> Busan -609735
>> South Korea
>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>> Mobile no. - 010-5818-3680
>> E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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After running the simulation I checked the trajectory in using ngmx in some
other system .. and it was working .. since I need to do some more analysis
during trajectory run on my protein I thought of running into VMD and I used
the file .trr after completng the simulation .


-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
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