[gmx-users] trjconv - PBC

[Steven Neumann]

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.

thank you in advance

Steven

On Mon, Oct 24, 2011 at 3:26 PM, Steven Neumann <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>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> 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>
>> wrote: > > Hi, > > You don't n...
>>
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