[gmx-users] trjconv - PBC

[Justin A. Lemkul]

Steven Neumann wrote:
> Last question:
>  
> I would like to visualise my whole trjajectory looking at one of the 
> ligands only which stacked to the loop of my protein. Which option of 
> trjconv will be suitable to see whole trajectory of this ligand withoout 
> any shifts on the screen so I will be able to produce a movie? I assume 
> I need to use ndx file of this ligand.
>  

trjconv -center

Select the ligand as the group to be centered.  This approach may not work well 
if there are large changes in position over time, so I'm guessing a bit. 
Otherwise trjconv -fit may work, or centering on some suitable group with which 
the ligand interacts.

-Justin

> thank you in advance
>  
> Steven
> 
> On Mon, Oct 24, 2011 at 3:26 PM, Steven Neumann <s.neumann08 at gmail.com 
> <mailto:s.neumann08 at gmail.com>> wrote:
> 
>     Thank you both!!!
>      
>     Steven
> 
>     On Mon, Oct 24, 2011 at 3:01 PM, Tsjerk Wassenaar <tsjerkw at gmail.com
>     <mailto:tsjerkw at gmail.com>> wrote:
> 
>         Hi Steven,
> 
>         Output can also be .pdb or .gro
> 
>         Cheers,
> 
>         Tsjerk
> 
>>         On Oct 24, 2011 3:59 PM, "Steven Neumann"
>>         <s.neumann08 at gmail.com <mailto:s.neumann08 at gmail.com>> wrote:
>>
>>         Sorry guys but I do not get this...
>>          
>>          
>>         I used:
>>          
>>         1. First make your molecules whole if you want them whole
>>          
>>
>>         trjconv -f md2.trr -s md2.tpr -pbc whole -o md2whole.xtc  (I
>>         have chosen my whole system for input and output)
>>
>>          
>>
>>         2. I do not need cluster anything
>>
>>         3. Extract the first frame from the trajectory as reference
>>         for removing jumps if you want to remove jumps.
>>
>>          
>>
>>         trjconv -f md2whole.xtc -s md2.tpr -dump 0 -o
>>         md2wholeDUMP.xtc   ???
>>
>>          
>>
>>         I did not obtain any coordinate file as output can be only
>>         trajectory (trr or xtc file)
>>
>>          
>>
>>         4. How to use this frame in:
>>
>>          
>>
>>         trjconv -f md2wholeDUMP.xtc -s md2.tpr -pbc nojump -o
>>         md2wholeDUMPnojump.xtc ?????
>>
>>          
>>
>>         Please, help!
>>
>>          
>>
>>         Steven
>>
>>          
>>
>>          
>>
>>
>>
>>         On Mon, Oct 24, 2011 at 2:49 PM, Tsjerk Wassenaar
>>         <tsjerkw at gmail.com <mailto:tsjerkw at gmail.com>> wrote: > > Hi,
>>         > > You don't n...
>>
>>
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> 
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-- 
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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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