[gmx-users] unfragmenting molecule in a trajectory

Irem Altan irem.altan at duke.edu
Wed Feb 1 21:18:35 CET 2017


For this I tried to do use the unfragmented configuration with the -s flag to trjconv when generating the trajectory. This results in a properly fragmented molecule, except for a single ILE residue. 3 atoms of this residue somehow remain displaced by the box size, while the other atoms of the same residue are correctly placed onto the protein. Is this a bug? If so, is there any way to circumvent it? (I use 5.1.2)


> On Feb 1, 2017, at 1:55 PM, Irem Altan <irem.altan at duke.edu> wrote:
> Hi,
> I ran a simulation using the output of another simulation. While obtaining this output, I failed to use the -pbc nojump option, so the initial structure for my simulation is a fragmented molecule. This resulted in a trajectory that I can’t unfragment using -pbc nojump. Is there a way to use a file that is the input to the first simulation in order to unfragment the molecule in the second trajectory?
> Best,
> Irem
> -- 
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