[gmx-users] -pbc nojump failure

[Irem Altan]

Hi,

Thanks. If I do that, the reference structure would be what’s in the .tpr file, right?

Best,
Irem

> On Mar 31, 2016, at 8:22 AM, Francesco Carbone <fra.carbone8 at gmail.com> wrote:
> 
> You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump) later.
> 
> Cheers,
> 
> Fra
> 
> On 31 March 2016 at 05:45, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 
>> Hi Irem,
>> 
>> Check the structure in nvt_water_frozen.tpr:
>> 
>> gmx editconf -f nvt_water_frozen.tpr -o ref.pdb
>> 
>> Cheers,
>> 
>> Tsjerk
>> On Mar 31, 2016 00:04, "Irem Altan" <irem.altan at duke.edu> wrote:
>> 
>>> Hi,
>>> 
>>> I am simulating a protein in its unit cell. I use the original .pdb file
>>> as an input, so the initial molecule is not fragmented. At the end of the
>>> simulation, I generate a .pdb file containing the trajectory of the
>> protein
>>> as follows:
>>> 
>>> gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc
>>> nojump -o prot.pdb
>>> 
>>> Despite the fact that I use -pbc nojump, I still get all the coordinates
>>> wrapped into the unit cell, and therefore the protein fragmented. What
>>> could be wrong? (I use GROMACS 5.1.2)
>>> 
>>> Best,
>>> Irem
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