[gmx-users] HI

[Justin A. Lemkul]

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pavan payghan wrote:
>     I have to recreate .gro file from .trr file by using trjconv which i 
> have deleated previously for disk  space reasons ,  im using following  
> commond for that
> 
>             trjconv -f full.trr -s full.tpr -o fullout.gro .
> 
>    so my question is will this commond give me the same gro file that it 
> was previously or it may variate
>     or any changes that u suggest in the given commond.
> 

No, this will give you the entire trajectory in .gro format, which is likely a 
very large file.  Use gmxcheck to see for yourself.

>     my second question is regarding g_rms,
>     i created the .xvg for  g_rms , the grph shows  it has  continous 
> run for molecule with some peaks in  between why is it so as im doing 
> analysis for the first time i dont know what does this indicates .
>  is it because  the molecule is jumping across the box ? so that more 
> rmsd at that place
>   ,i think by using -nojump i can do this  ?
> 

That depends on what you define as a peak.  Small spikes may or may not be 
reasonable, depending on what your structure is doing.  If these spikes are very 
large, they could correspond to your molecule crossing PBC, in which case you 
would have to use trjconv.

-Justin

-- 
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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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