[gmx-users] unfragmenting molecule in a trajectory

[Irem Altan]

Hi,

I was doing

gmx trjconv -f nvt.trr -s em.gro -pbc nojump -e 100 -dt 100 -o test.gro

I verify that em.gro is intact. nvt.trr is the output of a simulation whose .tpr file was created by a broken molecule. 

In any case, -pbc mol with the .tpr file works.

Best,
Irem

> On Feb 1, 2017, at 4:45 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> On 2/1/17 3:18 PM, Irem Altan wrote:
>> Hi,
>> 
>> 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)
>> 
> 
> Without an exact sequence of commands, it's impossible to tell what may have happened.  It is extremely doubtful that trjconv has a bug in simple PBC routines.
> 
> Reconstructing "broken" molecules should be trivial with trjconv -pbc mol and a .tpr file passed to -s.
> 
> -Justin
> 
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> Justin A. Lemkul, Ph.D.
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