[gmx-users] Removing PBC from Replica Exchange Trajectory

Yang Ye leafyoung81-group at yahoo.com
Wed Mar 14 20:38:08 CET 2007

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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