[gmx-users] Removing PBC from Replica Exchange Trajectory

[Yang Ye]

May not be a residue, just pick an atom in the center residue.
Have a try and hope you succeed.

Yang Ye

Thanks for Tsjerk's input. Rob, please make sure that that portion of
DNA is always binding together. Since you have a ssDNA, just center the
center residue.
mol was a non-existing option. It sounds meaningful =) Just use whole,
please.

Regards,
Yang Ye

Tsjerk Wassenaar wrote:
> Hi Robert,
>
> Maybe it's a bit nasty, but you may try the following, assuming that
> your ends stay a bit together:
>
> 1. Translate your system such that the last atom of chain A is
> centered in the _rectangular_ unitcell.
> 2. Generate a .tpr file from the translated system
> 3. Convert the .tpr to .pdb
>
> Gromacs places molecules in the box based on the first atom. Since
> you're dealing with DNA, your chains will be head to tail. Placing the
> tail of chain A in the center would mean that there's a periodic image
> of your chain B which has its first atom in the center. This image
> will be chosen during the generation of the .tpr file. Converting the
> .tpr to .pdb should give both chains close to each other. Processing
> the trajectory will be another thing...
>
> Tsjerk
>
>
> On 3/15/07, Robert Johnson <bobjohnson1981 at gmail.com> wrote:
>> I made an index file that contained the middle portion of the DNA
>> strand. I then used the -center option to center this middle portion
>> in the box and then outputted the entire molecule. However, the
>> molecule still appears broken. What is this -pbc mol option? That
>> doesn't seem to be one of the available pbc options.
>> Bob
>>
>> On 3/14/07, Yang Ye <leafyoung81-group at yahoo.com> wrote:
>> > A rather simple but effective way is to make an index which 
>> contains 1/4
>> > of your protein file. Use trjconv with -center tric -pbc whole/mol to
>> > center that 1/4 of your protein and output the whole protein.
>> >
>> >
>> > Tsjerk Wassenaar wrote:
>> > > Hi Bob,
>> > >
>> > > You could try -pbc cluster. If that doesn't work, it'll be 
>> difficult.
>> > > The option -pbc nojump will only work on continuous trajectories.
>> > >
>> > > Cheers,
>> > >
>> > > Tsjerk
>> > >
>> > > On 3/14/07, Robert Johnson <bobjohnson1981 at gmail.com> wrote:
>> > >> Hello everyone,
>> > >> I'm trying to visualze the conformations of a ssDNA molecule 
>> obtained
>> > >> from a
>> > >> REMD trajectory. As expected, there are parts of the simulation 
>> where
>> > >> the
>> > >> oligomer is broken due to the PBC wrapping. I've been trying to fix
>> > >> this with
>> > >> trjconv. However, the -pbc nojump option doesn't work - it actually
>> > >> makes the
>> > >> broken portions of the molecule worse and gives a terribly 
>> distorted
>> > >> trajectory. Since the REMD trajectory isn't continuous (i.e. 
>> there are
>> > >> instaneous jumps in the coordinates associated with REMD swaps), 
>> the
>> > >> nojump
>> > >> option may have problems. Does anyone know of any other way or 
>> other
>> > >> tools that
>> > >> I could use to reassemble my broken DNA strand?
>> > >> Thanks,
>> > >> Bob Johnson
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